Or it could be that there is an issue in 9.00 that is seemingly intermittent and random (as all bugs are, until understood), in which case the first course of action is to recompile with optimizations off, runtime checks on, instrumentation on, logging on, which will generally expand the exe and usually flush out (or sometimes, "fix") the issue.
You might wonder how the heck turning supposedly benign things like instrumentation and logging on could possibly "fix" an issue if they are not altering the logic of the application code in any way. The easiest-to-visualize explanation is that the instrumentation and logging takes time, and the full applicable folk wisdom here is:
Time heals all wounds, and some bugs too ;-)
Eg, if the program is measuring elapsed time between two events, then the extra slowness might be enough to eliminate cases of elapsed time (apparently) = zero, by stretching them out to be greater than the timer minimum resolution. Or to stretch out UI updates to be across frame updates, and that happens to reorder blits such that a copy from an complete image on one frame is now being made from a completed image of the following frame.
Whatever the reason for the size increase: don't panic yet (it doesn't sound like you are, but... just in case). Erel's track record is that critical issues within his domain are usually resolved immediately, and sometimes even quicker.