Ok, so im a somewhat experienced guitarist, and ive been playing for roughly 5 years. However im just now starting to learn theory with the help of the Crusade, and right now im working on my intervals. However, i dont understand why Ab to Cbb is a diminished third, but B# D## is a major third. It seems as though it should be augmented. Are there certain rules to certain intervals?
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yes, there are rules for all intervals. there's a big stickied thread about theory etc. i believe, so maybe give that a look over.

but as you your specific question, think of it this way
A to C is a minor third. Therefore Ab to Cb would be as well (they're both lowered half a step)
Now lower the C again, Ab to Cbb, it's now diminished.

B to D is a minor third as well. Raise the D a half step, and B to D# is a major third.
Raise both notes, B# to D## and you still have a major third.