OK, your problem is that with SSM /data/app is on one partition, /data/dalvik is on the second partition and /data/data (and the rest of /data) is on the internal memory
When you switch to data mode it mounts the first sdext as /data. Now the problem is that for user apps to work properly, they have to be in /data/app. Data mode created all the /data folders on the sdext but its not smart enough to move the apps into the /data/app folder. So, all of your apps are now in /data and /data/app is empty.
In addition, all of /data/data ( your app data ) is till on the true internal memory. This includes all your texts, settings and misc user data.
So basically, its all there but not in the correct place and there is no (simple) way to make it move to the correct location.
This is the PRECISE reason that kouma says you have to wipe the sdext (and basically factory reset) when you switch modes. In addition to not being to use the apps that are stored in the wrong location in the sdext, they are still stick there taking up the space that you allotted for /data.
When you do an advanced restore of your sdext, it just moves the apps to the root of your sdext, not into the /data/app/ folder.