System.Data.SQL Timeout expired

Hello,
for some time we have the problem that we cannot clean the WSUS database
from client entrys later 30 days.

With the APISample Tool CleanStaleComputers we get the error

.... Details: System.Data.SQLClient.SqlExcdeption: Timeout expired .....

we use WSUS2 SP1 and SQL2000 Database (8.00.818 - sp3)

Thanks for any response