USB to PC-Connection: no access to build-in storage but access to SD-Card and a lot of apps can't be started after(!) disconnecting until rebooting the phone

I use 1.6 and the storage upgrade. So: I only can see the internal storage with USB with MTP only. In the internal storage whatsup has a specifc directory “Whatsup” which is visible with MTP. And in it there are the three directories “Databases” “Media” and “Profile Pictures” containing the whole user content.