Alright, no offense, but YOU NEED TO BE MORE SPECIFIC! Because TP works, it seems like you are missing some IOS's required for the game to run. You mentioned cISO so im thinking you mean cIOSCORP... Anyways did your installation of cIOSCORP require for you to install the wads manually, or did it come with an installer which did it for you? In the second case, could you read me off the files in the cIOSCORP folder at the root of your SD card? It would help us immensely!
But before you do ANYTHING, pop in all of your games and list to us whether or not it is a backup. Example:
Twilight Princess - Retail - Works
CoD WAW - Backup - Doesnt Work
By telling us which games are giving issues, we can possibly see what is missing from the wii so that you can play it...
One last request - If you turn starfall's skip disk updates off, do the trouble games ask for you to update?