My application makes some easy operations: 1) Creates temporary folder. 2) Starts another application (using pipes) that writes some file. 3) Then my application gets the size of that written file. If it doesn't, the message box appears. 4) Deletes temporary folder. Sometimes the 3) shows message box (because the file is not closed yet) but it's ok. But the problem is when the 3) and 4)are not executed and application returns. This problem appears only on Win 2003 Server (on XP everything is ok). What's the problem?

It crashes sometimes, not every time. The code is hard to understand because many modules interact. I can show the code without interaction:
CreateTemplateDir("code");
RunCompiler();
WriteJad();
FullRemoveDir("code");

I think there's something wrong with commonly used dirs (one dir cannot be deleted when other application looks through it).