I would start over again with a clean install and use the ROM for a while without installing anything to make sure you have a good download.
Second I would install the apps that your having a problem with directly from the market.
Then you can do a batch restore in titanium and tick the box at the top that says "app only". Then I'd only restore data for apps one by one that you actually need the data for (games, wifi, etc). Any other app I'd manually log back into (Facebook, phandroid, twitter etc). You also want to go through the list of apps that titanium is restoring and make sure it's not going to restore anything from froyo(2.2) system preferences or anything from HTC sense.
I'm not too sure of saving settings with CM, every time I've used it, I was coming from a different ROM and would of had to set everything up again. And I personally prefer to manually set up everything each time, gives me a chance to clean up clutter, and I don't change ROMs that often. The process I described above is the way I install every ROM, and I RARELY ever have a problem.
The Netflix app is one of the main culprits of the "low on space" error seen on stock roms and unrooted phones. That error manifests itself in a different way on AOSP ROMs by causing force closes which is why my first recommendation was to clear your caches.