You could upload the vi in question so we can see what's up.
Sounds like you aren't putting a "reset" segment into your program, such as a frame at the end that sets the AO's to 0V.
Run vi->Set AO to 5V->Do stuff->Set AO to 0V->Shutdown vi.
MAX well reset the AOs when it opens up, so you need to do the same within your program.
2006 Ultimate LabVIEW G-eek.