There is some overlap in some of the official guide questions and GMATPrep, this is widely known here.
Consistency is good, I wouldn't worry too much as long as you're fairly consistent (this also gives you a solid grounding to make improvements as your weak areas are also consistent).
This happens as the GMAC is becoming more and more picky about what content makes it to prep materials. It has a large pool to use from, but is very selective to ensure questions do not have a bias on dialect (i.e. "toned milk" = "skim milk" in India) and convey what a test taker can expect from a real question.
We've been told with the new version of GMATPrep (coming out next year), this should no longer be an issue.
Thanks,