Here's a way to do it with a formula, although there are so many parentheses in this equation I'm about to go cross-eyed.

Since the rightmost two digits in your custom format represent the seconds, we can separate them using RIGHT(). Then subtracting that from the original number gives the "minutes" in your custom format.
I'll start out with the pieces, and then build the formula from its parts.
Convert B to Seconds = (60*(B2-RIGHT(B2,2))/100)+RIGHT(B2,2)
Convert A to Seconds = (60*(A2-RIGHT(A2,2))/100)+RIGHT(A2,2)
Difference in Seconds = ((60*(B2-RIGHT(B2,2))/100)+RIGHT(B2,2))-((60*(A2-RIGHT(A2,2))/100)+RIGHT(A2,2))
Now to convert back to the original format:
1. Divide the difference by 60, truncate it, and multiply by 100 to get the minutes part.
2. Divide the difference by 60, and take the modulus to get the seconds part.
3. Add 1 and 2.
Minutes Part = 100*(TRUNC((((60*(B2-RIGHT(B2,2))/100)+RIGHT(B2,2))-((60*(A2-RIGHT(A2,2))/100)
Seconds Part = MOD((((60*(B2-RIGHT(B2,2))/100)+RIGHT(B2,2))-((60*(A2-RIGHT(A2,2))/100)+RIGHT(A2,2))),60)
And here's the entire formula:
=100*(TRUNC((((60*(B2-RIGHT(B2,2))/100)+RIGHT(B2,2))-((60*(A2-RIGHT(A2,2))/100)+RIGHT(A2,2)))/60))+MOD((((60*(B2-RIGHT(B2,2))/100)+RIGHT(B2,2))-((60*(A2-RIGHT(A2,2))/100)+RIGHT(A2,2))),60)
Whew! Hope this helps.