no,flashing gapps after the fact shouldnt have anything to do with it. im really not sure what could be going on here. you do have background data and auto-sync turned on in accounts and sync,yes?
heres something you can try if you feel like flip flopping between backups.
-restore a backup that has all the apps you want.
-get titanium backup if you dont have it
-open titanium,go to: menu softkey/more/market doctor. touch ok to run the market doctor. it will go thru all your apps and verify their links to the market. if it finds some that are broken,it has some magic way of finding and fixing them.
-after its done,go to the market. download or update an app. this will cause the market to refresh. afterward,you should see all your apps in the "my apps" section.
-now wipe and go back to your current rom. go to the market. hopefully your apps will be there and be downloading. if they arent downloading,hopefully at least they will be there. im not sure how you might kick-start the market to download,if it isnt doing it. maybe force stop it and then go back in to my apps?
i personally dont care if my apps auto download or not,i can see both sides of the coin why some folks like it and some dont. i just wait for the market to download what its going to(even if that is none

) then run a titanium batch for "missing apps+data" so that tibu restores whatever the market didnt.
but anyway,hopefully the market doctor may work for you.
