Without directly answering your question (since I suspect the debugger's internal workings may not really be the problem), I'll offer two possible reasons this might occur that I've seen before:
First, your program does pause when it hits a breakpoint, and often that delay is enough time for something to happen (perhaps in another thread or another process) that has to happen before your function will work. One easy way to verify this is to add a pause for a few seconds beforehand and run the program normally. If that works, you'll have to look for a more reliable way of finding the problem.
Second, Visual Studio has historically (I'm not certain about 2008) over-allocated memory when running in debug mode. So, for example, if you have an array of int[10]
allocated, it should, by rights, get 40 bytes of memory, but Visual Studio might give it 44 or more, presumably in case you have an out-of-bounds error. Of course, if you DO have an out-of-bounds error, this over-allocation might make it appear to be working anyway.