Parameters will not stay "un-designated"

Since our implementation of Windchill our parts and assemblies have been riddled with conflicts.

We have now realized these conflicts are because, at implementation our start parts had all the User defined parameters checked "designate" even though only 10 have corresponding attributes set up in Windchill.
As we try and fix this we are running across a large number of parts which the parameters WILL NOT stay un-designated.
We uncheck the designate boxes on the parameters with NO corresponding attributes in windchill but as soon as you hit save it automatically checks them all again. 
Only on some parts and we have yet to find a common trigger among them that may be causing it.