As this is something that should not happen, I'd take a look at the following,
1) Is the SQL on or off box? On-box SQL is generally preferrable for GSS where possible
2) What is the SQL loading like, and what are the general resources looking like on the GSS box?
3) Do you have any custom SQL which might interferring with normal GSS DB activity
4) How many clients do you have, and are you using SQL Express?
In short my first stab without firther details is that something is amiss here in either the scaling of the solution or the implementation.
Kind Regards,
Ian./