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There is one other thing that I can think of: when running the program (not debugging it), is it the same build as the one you are stepping through? That is to say, your debug one is obviously 'Debug', but when you're testing it without stepping through it are you still using the 'Debug' build (as opposed to the 'Release' one)?
You probably are, but I just wanted to put this out there: there's a number of times where I've had problems with the 'Release' build but not the 'Debug' one... some things like bad memory access and the like that 'Debug' apparently is OK with.
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