I stumbled on this while making a mission which regularly deals with large numbers (the costs related to war) in it's calculations. The problem appears when you work with numbers > 16777216.
16777217 and above combined operators like % or == will give you some weird results. These are the only 2 operators I've managed to confirm as having this issue due to the fact that numbers are converted to scientific notation when converted into strings or put into the rpt-file.
Script file containing 2 tests that show the problem.
https://dl.dropboxusercontent.com/u/74011028/bug.sqf
According to the community wiki on the data type Number (http://community.bistudio.com/wiki/Number) the game is supposed to be able to atleast manage very large numbers