Double check to make sure you don't have bedside mode enabled and in fact have the show clock when charging.. If you do and it doesn't than this is something a lot of people started to notice after the 5.0 software was pushed out.
Do you have software 220.127.116.113?
Right now this is sadly something that we just have to wait for RIM to fix in an update. You could try to pull the battery a few times and see if it ever works correctly but for the most part I've found it just doesn't work as intended
I had version 5 but upgraded to version 6 hoping that it would fix the issue. It didn't. I just wondered if there was a setting somewhere that I had missed. From your response, it appears that there isn't. I guess I'll just have to live with it.
Checked with a couple of users over at BBTweaks, one has a VZW 9650 with OS 6, and their consensus is that it is not a problem with OS 6. So it is either a bad install or something in your settings is not set correctly. Specifically, the user with a 9650 running OS 6 said his bedside mode works fine.