Theme options don't work on mainsite but on the subsites it works

Hello there..i seem to be having problems on my mainsite. I tried 2 different 3rd party theme.All the theme options and settings seems to work on the subsite(subdomain) but i can't use the theme options on the main site..anyone having this problem before?..i tested the catalyst framework and it seems to work on the subsite as well but just won't work on the mainsite.
Example problem..Uploading logo image> the image can be uploaded and i can see that it is stored...but it just wont save on the settings.However on the subsite it just work as normal.