I can not say what a cause would be for your permissions issues. I can say this is not a common problem, lots of people install OMLx without such issues.
A possible way to trouble shoot this would be to reinstall with a fresh formatted /home partition and see if there are any permissions problems before adding files from the old Windows installation. If there are that would point to a possible corrupted .iso file download or a corrupted copy to installation media such as a usb flash drive. For example if people use Rufus to copy the installation image to flash drive that would cause problems unless Rufus was set to use dd to do the copy. Downloading with browser might lead to a corrupted download, this seems less likely though. This screen shot is from the ROME Release Notes:
Then add the files saved from the old Windows installation one at a time and see if any of these lead to such problems.
There is more information about this stuff in the Forum Resources section and the OM Wiki. If you have not read the Release Notes and Errata for ROME you should do so. For Cooker there is this. The Release Notes and Errata for ROME generally apply to Cooker as well. Rock has it’s own Release Notes and Errata, I am not sure what you are currently using.
IMO our documentation is not perfect or as well organized as it might be. We are a small all unpaid, volunteer, group so what we are able to do within those constraints is what we are able to do.
If you choose to install ROME at this time you need to follow this article. We hope to have these problems fixed soon with the next major ROME upgrade.