About a month ago, Google acknowledged there was some kind of issue with Android Market whereby installed apps weren't being listed in the My Apps section, which prevented users from determining what apps needed to be updated. Not sure if it has been resolved so far.

I had been running Royal Ginger 3.0, which had been working fine; but I decided to switch to CM7.1, and that's when my issues started appearing (only half my installed apps were showing up under My Apps.

As soon as I restored Royal Ginger, everything was back to normal.

In the meantime, you can use AppBrain to determine what you have installed and what apps need to be updated. The problem is that you cannot do batch updates, and it also picks up paid apps that you get from Amazon's Free App of the Day (whereby updating in Android Market will incur a charge).