I don't know why your database is acting as it is, but here is a link to performance tips
that you can check.
Do you know if there is appropriate indexing on fields? Sequential reads can be a nightmare in any dbms.
Do you have test data to identify any specific function/procedure...?
Have you tied putting some comments/messages re "in this procedure at time..." and done any analysis?
Have you had any network or sql server people check any of their monitoring tools?
Did this particular database ever run faster than it is currently? If so, what changed?
Has anyone talked to the third party developers for ideas/suggestions?
may be relevant, you can see what others have experienced/done.