Mats,
I have no idea about your error, it does not look like anything mojoPortal would do. When site settings are saved, we touch a cache dependency file to clear the site settings cache, but that file is located under /Data/Sites/[SiteID]/systemfiles
The path in your error is very strange, maybe your host can explain it, possibly they are using virtual directories that point to strange locations.
Thomas,
Your error looks more likely to be caused by upgrading but failing to upload all the files so some files are not the correct version. I would re-deploy the files and watch carefully for any ftp transfer errors and retry them until all the files make it.
Hope it helps,
Joe