[revenge8]

check the media section in manage applications.. make sure nothing is checked. Some apps that are moved to the media section randomly disappear after reboots whether you are rooted or not. This is a known bug. Move all apps to internal memory until a fix is given. Hope that helps.

Also there is a known problem restoring/installing system apps. It seems extremely difficult and I'm not sure if anyone has successfully restored system apps with TiBu yet.

 

[revenge8]

welp hopefully you made a nandroid backup of your stock ROM before you installed the custom one. You may just want to go back to that.. then reinstall the custom ROM.. something seems like it went wrong in the install process. I cant think of any reason why your apps wouldnt show up
Also there is no option "to set a certain setting to access internal SD or External SD to have them populate my applications list" as stated in your OP.

maybe someone else will think of something.. but ill keep it in my mind and see if i can come up with another reason or fix for ya

 

[revenge8]

you can always try to uninstall all your apps and reinstall them all cleanly... try not to use TiBu just do everything through market. Either that or just start over again like i said and reinstall your custom ROM from a clean slate.