It seems that CustomNPCs and Immersive Engineering assemblers do not like each other and it seems that using CustomNPCs and the assembler just borks the assembler so far.

I have not tried this in my custom mod pack but in FTB Revelations it seems to brick the assembler. It doesn't produce any crashes it just does not work.

It seems some new patch has already fixed the issue nevermind sorry for wasting your time.