Question [Q] root present, device custom but no root access

I have a previously rooted S3 that had permissions mostly stripped after 4.1 update (a while ago) and now I'm trying to "re-root". Root checker says it is rooted and the device status is "custom", but superuser cannot get root access therefor I cannot get rid of the remnants of the old root and apply the new one. Any help would be greatly appreciated!!!