My site has one library and various folders in it which are given access through various groups and different permission level. Yesterday I got to encounter this scenario that no user from any group is able to access the site though read/edit permissions are given to the user through the group he belongs to.
I, as a site collection admin provided read permission to a group(JapanCAO) on library and its folders and sub folders. Later I added my colleague in that group. Now on pulling up the group's permissions, home and folder url's have read access. But while my colleague navigates to the url's, he gets message
"Sorry, you don't have access to this page".
Now I reversed the scenario. I set my colleague as admin and removed him from the group(JapanCAO). I removed myself from admin list, and added my name into the group(JapanCAO). Strangely I am able to access the home url and also all url's having read access for the group(JapanCAO).
First I thought this issue might be because of the multiple copies of master pages i created some days back. but on resetting the changes to site definition, the issue still exists.