My experience with Win98 is that it is not a very stable system, regardless of software used. For example, Win2000 and XP are far more stable than 98. I've had it crash on its own if I leave the computer on for several days.
I wouldn't recommend running programs for long time (few days) on this OS.
This being said, can you be more specific in your question. What kind of stability problems did you have, which VIs did you run (if possible post them here), did you change the interrupts and priority levels on those VI, do you get error messages or blue screen....
Zvezdana S.