Hey guys,
I know this is an old post but got to it as I had the same problem. I have now managed to fix it and hopefully it will help you and others with it.
Test if its a hidden file problem:
Install Quickpic, which is a great photo app, works fast too, and also shows you if there are any "hidden" pictures. If this is the case then you need to install Root Explorer (your phone needs to be rooted).
Fixing the problem
1. Install Root explorer
2. Browse to your picture folder (on the San Francisco it is the DCIM folder).
3. Long press on it and change permission. For some reason the change in permission is what prevents other programs from finding it.
4. Allow user to read, write and execute the files.
5. Check if your pictures are being detected now
Job done!
Hope that helps