Are you opening references of any sort (TCP, VISA, FILE, ActiveX...) without closing them?
Do you have structures that get bigger over time (like arrays).
The decrease in performance sounds pretty severe to me (on the scale of 50-100 times more). Does it continue to deteriorate?
If all this didn't help to point you in the right direction, you can post all your files. Click File>>Save with Options and select Development Distribution. All your VIs will be saved into an LLB file, which you can upload.
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