I contacted PR's customer support about these issues a few weeks ago....If you're seeing repeat questions, it could be one of two things: you either deleted your previous test(s), or you're taking the tests on different computers. The software is set up to remember which questions you've been given, and as long as you don't delete the previous tests you've taken, and take them all on the same computer, you shouldn't see duplicate questions. If that's not the case for you, then contact customer support - that will get you a lot farther than complaining in the forums!
On the timing issue...if you take each section separately, rather than taking it straight through like the real GMAT, the don't know if they corrected it for later 2004 releases. So I would take the test straight through. Better to do that anyway so you can work on your stamina for test day.