Are you using VISA? It might be doing a VISA initialisation when starting. Maybe you changed something to do with VISA calls. I've had this problem in the past, but I can't remember off hand how I got around it. The code's at my last job, so I can't check. Sorry.
Other problems may be saving the VI with large data sets set to default in indicators or controls which slow down the program loading, but this should be visible on the EXE size.
Hope this helps
Shane.
Using LV 6.1 and 8.2.1 on W2k (SP4) and WXP (SP2)