Persiistant connections can slow down a server if it does not have enough memory since each connection takes a chunk of memory and if you have a few hundred open connections this can add up real quick.
You might want to take a look at my previous reply for some things to check on where the bottleneck might be and how to configure one of the options for best performance.
The scripts have been heavily optimized with indexing in place on the database. Normally slowdown comes from the sql server as with several hundred open connections the mysql server can be doing several hundred queries in a matter of seconds.
