"We are violating MANY pilots for not staying on the RNAV tracks. Right now they are trying to figure out if it is pilot error, equipment or software"
Either you worded it poorly or its a piss poor way to operate. Violate (again, an ASAP gets me out of 99% of what controllers try to get pilots on) then investigate is ass backwards.
Investigate, then make the determination.
BTW, ATC does not violate pilots.