I am running Project Elite and it is a great Rom. My problem is not Rom specific as it has happened to me on SS, Sapphire and Project Elite.
Following any reboot, all of apps on SD are not available, and only show the default green icon. Back when I used Launcher Pro, I would just keep restarting it and the apps would eventually come back after several LP restarts. I am now running ADW (with zero redraws), but the apps do not come back with the launcher restarts. I generally must reboot the phone numerous times and eventually, they come back, but this process sometimes takes several hours or longer. I do not know if it is OS related, ADW related, or an issue with the SD card (which seems to work fine otherwise). The amount of downtime I experience with this process is becoming a significant problem for me, and would really like to resolve this.
I also notice that when I am in this state, the apps all show up in the "Settings, Manage Applications", but are greyed out. During this period where the apps are accessible, I can still access content on the SD card through Astro, Root Explorer, etc.
I notice when I click on any application (including ones in internal memory), in the manage applications menu, it will just hang and never give me the file size, data size or cache size. I must do a force stop to get out of the settings menu. Lastly, in this state, I can not install any applications from the market, update any apps from the market or restore anything with Titanium. So something seems to be going on that is effecting more than just the apps stored on the SD card.
One final observation/question, I never created an app2SD partition on my card. The apps move to the card and function just fine, once the phone eventually recognizes them, but didn't know if this was somehow contributing to my issue.
Any suggestions would be greatly appreciated.