The problem is that a user has datareader and datawriter permissions on the databases, and is able to update all of the tables in the database, except for one particular one. When the user tries to update this table they get a timeout error.
The user believes it could have something to do with the table being locked.
Thanks for the tip gbritton, I actually ran the Activity Monitor as suggested and found that there were two different users connected to the database and in the "Task State" section was SUSPENDED, when they disconnected, everything seemed to work again.
No idea what the cause could be.
What I have found out in the meantime is that all users that have access to the database use Microsoft Access to do updates, inserts, etc.