There are multiple threads about this:
http://www.flyertalk.com/forum/showthread.php?t=747794
http://www.flyertalk.com/forum/showthread.php?t=749432
http://www.flyertalk.com/forum/showthread.php?t=747057
http://www.flyertalk.com/forum/showthread.php?t=763122

Since you already initiated the transfer from AGR to Choice, you should be in good shape (getting the original 5KAGR::25K Choice).
You will need to be patient. The points may post later this week, or they may take longer--don't forget that the terms tell you to allow 60 days for the transfer.

If you are trying to get WN credits from Choice, you will be unable to redeem your points for WN credits unless (or until) you have had a stay since 1/1/06 or have Choice credit card activity. If you are trying for WN, you should try to redeem your Choice points as soon as possible after the transfer is complete, because you never know if Choice will change the redemption rate for WN transfers.