I do find it takes a long time after startup to show all apps, and it can be a pain waiting, but the ones on sd do show up after a while. But I'm using app to sd app from market, and not partition or custom roms. If you're looking for some apks to apps you lost that were free on market shoot me a pm and Ill see If i have them or can get them. Also you can go to
https://market.android.com/ on your pc and have apps pushed to your device. I don't have the market apk to help you out with that. after you do get market to work, any market app you instal thru an apk, market wont see it.
also check
http://www.filecrop.com/android-Market-market.apk.html