Raven, I wish I had a great answer for your dilemma.
Perhaps someone will have a solution or sound answer as to why this is happening.
I have never taken classes for digitizing, but find John Deer fascinating.
I have his book, which addresses gaps, but it would not seem to apply to your designs as they are stitching out perfect in the original format.
Just guessing, but it sounds like it is in the software's translation from .art to the other formats. Great big DUH on my part?
Have you tried other brands of software - there are a few with free trials?
Pattiann