This ain't going to be easy or pretty but here goes.
Create a new VI. Drop half of your VI's in it.
Do the build and see if you still have the "issues". If so, one of the VIs you have included is the culprit. Toss half and retry. Continue until you find offending VI.
Once you know which VI is doing you in, we should be able to help.
I did not say this was easy did i?
Ben