It's not the call to .Count that's slowing it down. You've got two lines that appear to be loading entire tables, users and Services, then you iterate over the both both tables, the Services table every single time you look at the next user in the users table. You have a loop nested inside a loop and that's what killing your performance.
Next, you're executing this statement (Num user records * Num Services records) times:
this.cc.serviceAuthorizations.Any(p => p.UserID == alluser[i].UserID && p.ServiceID == allservices[j].ServiceID
That's going to take a while, PER ITERATION THROUGH THE LOOP.
I don't know what you're trying to do with this code, because I'm too damn tired right now to think, but it seems like this would be a solution better solved in the database and not iterating through a bunch of rows doing it in inefficient code.