FP5 is the one that has an occasional issue with “Preinstalled Apps confusion” which hasn’t been resolved or able to reproduced by our lead developer.
First a question: after your “preinstalled apps uninstall” did you reboot? And then again did you reboot after “preinstalled apps install”?
If so, then it must be related to this bug I note, if you read farther down the thread you link I got feedback from Vincent (lead dev) to reset your iodé app custom settings… There are a few extra comments there about making sure to “uninstall updates” to the ioDroid app, etc. that may be adding to the confusion.