Bear in mind that the EXE created is basically similar to an LLB. Therefore, you need to be careful with the paths, especially if they're relative.
For example, if you build an EXE from a vi in C:\Code\MyVI.vi, it generates an exe located at C:\Code\MyExe.exe. When running the code, however, the VI "MyVi" will have a path of c:\Code\Myexe.exe\Myvi.vi. In this way, the EXE behaves like a folder. Yes it's annoying, but it can't be changed. This means that many relative paths which are valid for a VI won't be valid for an EXE.
There have been VIs posted here which help get around that problem (Always returning the correct folder - minus the EXE). Do a search for EXE and Path, and there should be some examples.
Hope this helps
Shane.
Using LV 6.1 and 8.2.1 on W2k (SP4) and WXP (SP2)