I think I have found what all those problems came from:
Usually, with Android, you have several MTD partitions containing the various bites of the OS. One of those partitions is called DATA and this is where most of the stuff happens. Configs, non-system apps, libs for apps... all is there.
Now, with the IQ, there is DATA but there are also 2 other partitions: USER_DATA & PB_DATA. The thing I have noticed is that these are MMC partitions and not MTD and that some stuff in DATA is symbolic links to one of those partitions.
What are MMC Partitions? Think of them as partitions that would be on an SDcard. So, you have DATA (main partition) spliiting into 2 other partitions (USER & PB). When you Factory Reset, you only erase DATA and NOT User or PB... you can see why there were some problems now.
My plan is to remove USER & PB and only leave DATA as the only DATA partition. I think that should solve 99.9% of all the app & config problems we have on this.
I have actually set up a To-Do list for myself and will work hard to get this to work and learn the inner working of Android. After that, I think we might have some Gingerbread for lunch.