FUBAR-ed file from template

Hello all,

I have set up some base part templates, (flat, round, angle, square tube).
We use this same "method" for creating parts in IV and MDT. These templates
worked wonderfully in every release from '01+ thru '03.

The problems that I am having:

1. New part from tube template:
a. pre-existing, suppressed chamfers fail on unsuppressed, due to a
missing edge
b. pre-existing, suppressed chamfers, once fixed, still fail if tube
length is modified

2. If I edit a part created from a template, in an assembly, the mates on
that part lose the features that were picked for the mates.

These issues occur with both migrated and new parts when saved as template
files. The failing chamfer problems don't occur in the template file itself,
or in the file that the template was created from.

Any insight would be appreciated.
Ask any questions necessary to understand my problem.