The Controller and Boss Glitch, often shortened to C/B Glitch due to its length, is an MS Ruleset-exclusive glitch that affects the way teeth, bugs, and the paramecium behave when they attempt to exit a clone machine or trap. It is among the earliest documented glitches in CC1, being encountered earlier than even the Transparency Glitch.
The root cause of the glitch is uninitialized variables in the game. That is, some part of the program attempts to read some place in memory without ever writing to it first (or the programmer forgets to write to it first), causing the read data to be something unrelated that was coincidentally written in that place earlier by a different, unrelated part of the program.
In MS rules, when an affected monster attempts to clone, the direction it exits the clone machine will not simply be the direction the monster in the clone machine faces (as it is in Lynx). Instead, it will be determined by the last attempted direction of the last monster in the monster order, called the boss. Whenever a new monster is created, it becomes the new boss. Monsters that die are removed from the monster list.
If the monster list is empty, or if the boss doesn't attempt to move (e.g. a stopped tank), nothing will happen, but if the boss directs the cloned monster in an illegal direction, it also does not clone. If the move ever becomes legal, the monster will immediately spawn in that direction, even if the boss has changed direction.
Observe the following diagrams:
The bug will not clone in this situation.
With the fireball being the only monster in the monster list, the bug will clone R when its button is pressed. After moving a total of 2R 2U 2L DLD, it will hit the red button and be the boss of the bug it clones, which releases south.
In MS rules, when an affected monster attempts to exit a trap, the direction it exits the trap will not simply be the direction it was facing when it entered the trap (as it is in Lynx). Instead, it will be determined by the monster directly before it in the monster order (which can be replaced under specific conditions), known as the controller. If the trapped monster is first in the monster order, it is stuck forever. Teeth, bugs, and paramecia are affected by this version of the glitch.
Observe the following diagrams:
Nothing happens here, since no other monsters exist.
If the walker is ahead of the paramecium in the monster order, and it is pointed east, then when the brown button is hit, the paramecium will move R and DLU, back onto the trap. Although a thin wall is above it, the Concussion Rule does not have an effect on C/B Glitch monsters if their controller points in a different direction.
Here, however, with the walker pointed south, the paramecium moves D and LUR, which will smash Chip unless he dodges.
Immobile bosses or controllers
Unusual things happen to bosses or controllers which cannot legally move. A monster stuck in a trap will always work in that direction even when physically trapped (this is frequently used to avert glitch issues); however, when such a monster is released, or any other time one is blocked by acting walls, two categories of exceptions begin to arise.
- If left untrapped but immobile: the bug, paramecium, fireball, glider and pink ball will control or boss in the opposite direction they are facing; a teeth will work in the direction it is facing, a blob will work in a random direction, a walker will exclude its initial direction from the four, and most strangely a tank will not work at all as long as it does not move, rendering the trap or cloner dead. This mechanic is the cause of one of the rare C/B Glitch issues in CCLP3.
- If trapped, but released and now immobile: the bug, paramecium, fireball, glider, pink ball and walker will control or boss in their present direction, while the teeth, blob and tank still function the same way as before. Note that monsters that apply to the original rules of the glitch must themselves be released by their own controllers to function in this manner; if the trap is dead, the monster will still face in its current direction.
Monsters that attempted but failed to clone will not count as a possible boss; it is impossible for such a hypothetical monster to be a controller of one that already exists.
- Problems: The paramecium that controls the toggle walls that free the bouncing pink balls in the top section is trapped in the trap after it releases the first wave, and never escapes from that trap to release the ones by the chips because all the balls, including the trap controller, in the level move horizontally, and both horizontal exits from the trap are blocked.
- Nightmare: Five separate incidences of failed controllers.
- The bug at the very beginning of the level is controlled by the bug bouncing around with the red key, near the end of the level, which goes in all four directions. When the button is hit, the controller is moving south, which causes the bug to drop down and simply circle itself back into the trap. Since it is facing a wall when it is trapped, it will not move again.
- The paramecium past the four bombs is controlled by the boxed-in fireball above it, and it happens to be moving south when its puppet is released, usually causing this paramecium to also drop right back into the trap. Although the paramecium can be released and chase Chip, it usually doesn't.
- The teeth in the lower right corner is controlled by a pink ball moving horizontally; both horizontal directions are blocked.
- The bug that gets stuck in the trap at the very end of the level is controlled by the one that is sixth in line, at [11, 11], which causes delay in its releasure when the brown button is pressed by Chip. This does not affect gameplay, as Chip would not be caught by the bugs anyway.
- Catacombs: Repeated occurrences of trapped bugs with controllers on clone machines cause none of them to work.
- Miss Direction: the teeth stuck in the trap at grid coordinate [14, 22] is controlled by a vertical tank, but the vertical escapes from the trap are blocked.
- All Full: The boss of the bug clone machine near the room full of computer chips is the ball bouncing left and right just below that, and the horizontal exits from the clone machine are blocked.
- Pain: The bug stuck in the trap is the first monster in the monster list, and will never escape its trap.
- Trust Me: The boss for the bug clone machines, but in particular the one just to the right of the exit, is a paramecium in the lower left corner, which doesn't move west for a sum total of  after the red button is pressed in the busted solution.
Occurrences of the C/B Glitch in CCLP2 are far more rare, since its mechanics had been well-documented by the time of release (2002); only two levels include it.
- The most major occurrence is Trapped, where the paramecium clone machine will occasionally clone, as its boss is a blob. If Chip can steal the blue key before the blob directs the cloning towards the east, which is the only free direction from the clone machine, he will escape the corridor and win in 5 seconds.
- The second level that can use the glitch is Dangers of Fire and Beasts, although it saves only one second and requires luck. Chip can gain an extra  by cloning two teeth instead of avoiding two red buttons and save enough of it to add an additional second to Chip's score, but this requires the walker controller to send one of the teeth south off a trap and into water.
Accidental cases of the glitch were all but eradicated by CCLP3's release in late 2010, but it is used intentionally as a level element in one case. One new type of the glitch was officially documented in June 2011.
- Two Sets of Rules is a two-part level with half the level solvable in MS only and the other in Lynx only, and three cases of trapped or cloned bugs are obstacles along the way.
- Some solutions to Go Back to Start involve the paramecium clone machine in the southwest room, which will refuse to work in MS if the trapped fireball at [8, 19] is released into the water, as the new boss is a non-moving, untrapped tank. The bold solution avoids this device in both rulesets.