I have now reproduced this on a small example.

I have added eweasel test incr348 for this bug.  This test case was
extracted from a real-world failure while working (not bug hunting).
Please fix this for 6.6.  The closest existing test I could find was 
melt091, but test incr348 does not involve any changes to library
classes (melt091 did involve changing library classes and then melting).

This is very frustrating.  I upgraded to 6.5 and I'm still running into bugs regularly
during everyday usage.