Maybe one of the soruces you have isn't loading or refreshing like it's meant to be.
Try accessing it without the internet connection, and disable the suspect source.
Maybe what is going on is that the folder where all your apps are installed is full, there is an app that moves all your installed apps to a different folder, this depends on the firmware version you are running on your iPhone.
If I was in your situation, I'll prefer to restore my iPhone and then install. Everything again, it's a little time consuming but will ensure a clean install.
Follow the instructions on this web: www.hackthatphone.com
Yesterday I restore mine and update it to 1.1.3 because I was having problems receiving phone calls, due to the 3rd party apps on 1.1.2 and I can't afford that during these days because I am applying to new jobs and I'll be receiving some important calls. Also I am expecting the new SDK apps that were promised for the end of this month, but it seems that they will be delayed...