Good question. Short answer: Yes, you are allowed, and no, it won't affect your chances of winning one of the prizes. But ...
Long answer: If you win a prize, a condition of collecting the cash is to release a fully playable version under a Creative Commons license or similar. So when the winners are announced later this year, if you've won, you could either ...
* Put a CC license on the game and make it free or pay-what-you-want, & collect the prize money
* Put a CC license on the game and just keep selling it anyway (technically there's no reason why you can't -- it does mean others can share the game elsewhere for free, but people can still buy it from you if they want), & collect the prize money
* Put a CC license on a lite version of the game only (such as a text-only System Reference Document), but keep selling the full version, & collect the prize money
* Take the fame & glory but decide not to take the prize money (in which case we'll create a new prize for somebody else
Submitting to the jam doesn't commit you to anything, so you don't have to make up your mind now.
