Could you give us some more information. You mentioned that you upgraded the computer, and it goes slower, but how much slower are you talking about? Do you know where exactly in your code it is that things are slowing down?
Since you needed additional PCI slots it could be that you
are trying to pass a lot of data on your PCI bus, if that's the case it could
slow things down, particularly if you have a PCI video card or something that
will eat up a lot of your bus's bandwidth.
A few more details about your application and the specifics of what's happening would help a lot in determining what is going on.