[SHOEBOX] "Morphophonemic form gives cyclical pattern..."

Hi all.  Josh here.

   Okay.  I was able to set up interlinearization that recognizes
conjugated word forms and it is working quite nicely.  In fact, I'm pretty
excited--this is the most organized Kartesian has been since its creation.
   But now I am presented with a problem AGAIN.  Upon interlinearizing,
many times a message pops up that says, "Morphophonemic form gives
cyclical pattern..."  And that is EXACTLY what it does.  It parses a word
giving it an endless cycle of alternating INCORRECT morphemes...  why is
it doing this?  Has anyone else received this annoying message?  Let me
know.  Also, I was wondering if it was possible to restrict certain
underlying morphophonemic changes to specific PARTS OF SPEECH.  Because of
the common use of various affixes for more than one reason (the affix -ee
has about five DIFFERENT uses which always clog up the Ambiguity menu),
things tend to get messy.  Also, is it possible that this is the reason
I'm getting that nasty message I spoke of earlier?  I hope so, and I hope
that there is a way to restrict underlying forms.

-- Josh :)