In our case, on ly one user was affected. Others were not. The curious thing is that there were no differences in their roles, i.e. My user has same privileges over EPRNext than the affected user.
I had the problem with Employees. I managed to solve it, but (BRACE FOR IT) I do not remember how I did it.
Now this user is having the same issue with tasks assigned by other users. He can see tasks fine, but tasks with assignment from others he cannot see.
Probable solution: Make sure to be logged in as Administrator whenever you change any permissions.
Even if the Role Permissions are set per doctype, just check to make sure they are.
Go to the user. Remove the roles. Save. Add the roles back again. Save.
This should restore visibility and unrestrict the doctypes.