Probably the permission thing prevented it from copying all the skin files to the new site during setup.

I would try copy all the files from /Data/skins to /Data/Sites/1/skins (assuming 1 is the siteid), this way if there aremissing files in the skins its will restore them.

Hope it helps,

Joe 

It might help to recycle the app pool after you copied the files.

The next step to diagnose it is to view the rendered source of the page, get the full url to the  ...csshandler.ashx?... and paste it in a new browser tab. Do you see css or do you get an error?

Hope it helps,

Joe 

Ok, what is th error? Is it logging a stack trace in the mojoportal log at /Data/currentlog.config? or Administration Menu > System Log

Newest errors are at the bottom so ignore all the errors except that. 

I think you must have tried to keep your old Web.config file instead of using the one that is included with mojoportal 2.2.9.6 or even 2.2.9.5.

Its true there is no file for csshandler.ashx but it does not need to exist because its declared as a handler in Web.config so any request for csshandler.ashx will be handled by the handler, but the handler declaration must be missing from your Web.config

Hope it helps,

Joe