[eluser]TheFuzzy0ne[/eluser]
Do you know exactly what queries are causing the slow down? Also, have you noticed any pattern? For example, is it happening at 10 past every hour of the day? If there is a pattern, there's a chance that someone else is doing something resource intensive with their tables, and that could be causing your problem.
The Session class's query is virtually always in the same format. Each query contains between 1 and 3 very simple where clauses, so it's unlikely to be the query that's the problem, it's more likely to be the database. The only other thing I can think of is that your table is not indexed properly.