I've seen this happen before. Don't know how to fix the underlying cause...but you can try this to at least get the module where you want it.

Go to the module's settings
Use Advanced Settings>Page Settings and move the module to a different page
Go back to the original page
Use Add Existing Module to add the module back to the original page in the desired pane
You can then Delete the copy that you put on a different page

Thanks for your reply but this is not a workaround if you have to reorganize multiple modules. Besides i think there is a big chance that there are more things that do not work properly or the way they should be. 

I hope find a proper solution.