Merging branches in SVN after converting with cvs2svn

I am hoping somebody has run into this before, but searching the mailing
list archives, I could not find a similar situation.

I have converted a CVS project to SVN using the cvs2svn tool (version
2.3.0).
Everything looked great after the conversion -- I was really impressed with
how easily everything worked.

My question is this:
I had branches in the CVS project that got converted to SVN branches.
However, now in SVN I cannot merge the branches back to the trunk without
old, extraneous files showing up and causing conflicts.

Is this a known limitation of the CVS to SVN conversion process? That
branches which were branched outside of SVN (and under CVS) cannot be merged
properly to the trunk?

If my question is not clear enough, I can try to provide better details and
examples.

I would be very grateful for any help or direction with this.

Thanks,
Christian

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