There are times when SharePoint can even deny the Site Owner to access his/her site. There are numerous reasons behind this issue but I just want to give you the solution. So here it is:
Step 1:
Run following stsadm command after replacing place holders, mentioned in <>, by actual values:
stsadm -o siteowner -url <YourSiteUrl> -ownerlogin <Domain\AnyValidUser>
Step 2:
Run following stsadm command after replacing place holders, mentioned in <>, by actual values:
stsadm -o siteowner -url <YourSiteUrl> -ownerlogin <Domain\SiteOwnerLogin>
Thats it. Now access the site by Site Owner user and you will be allowed.