It may well be that you're executing both programs in the UI thread. This means that if they're in the same thread, they basically can't both be "running" at the same time.
Would it be possible to throw the instrument communication into a sub-VI executing in a different thread (Instrument IO for example)?
Hope this helps
shane.
Using LV 6.1 and 8.2.1 on W2k (SP4) and WXP (SP2)