I had faced this similar situations long time back and drafted the solution somewhere in my mail and forgot about it. But again today I faced a similar situation and the I bugged the internet to get a solution but with very less help. I couldn't find the exact solution except for few pointers here and there. So I went back and dig out all my old mails .
I know many of you might have ended up in a similar situation where you by mistake "checked and unchecked" a permission which set a deny permission and this overlapped with another permission ending up in not letting the user access the content which he was supposed to access. Adding this solution here for those who might search the web for a solution for similar problem