WordPress 2.9.1 has been released and fixes those pesky issues with pingbacks and Scheduling posts that existed in release 2.9 that required you to update your cron.php to resolve. I upgraded to 2.9.1 on all of my blogs this morning and tested both a scheduled post and pingback to make sure all looked proper and I don’t see any issues yet. As always, make sure you backup your full wordpress installation prior to upgrades, it is better to be safe than sorry.
Good luck with the upgrade, I highly recommend you do it, especially if you were running WordPress 2.9
-Dragon Blogger