Mike,
I have experienced the same thing.
However in my scenario, i had 1 part 2 configurations.
The assembly accepted one of the configs and not the other. (suppressed the old one as you indicated)
Once i opened my newly renamed file in solidworks and did a replace and unsuppressed the item saved back to my workspace and checked in the assembly, the issue resolved itself and it opens correctly now.
I am not sure if this is helpful or not.
I am using 10.1 Windchill with SW 2012