For the record, if you had said anything to us earlier, or created a
support ticket we would have worked with you directly, via remote session if necessary to get this issue resolved and to have PT3 working properly for you. These performance problems are very rare and most likely have specific causes.
In your case, it sounds like you've likely been playing at Full Tilt Poker and PT3 has been unable to move the processed files out of your Full Tilt hand history directory. When there are 45,000 hand histories in the directory to be processed things slow down immensely. I'm confident if you closed down FTP and moved those files out of that directory to anywhere else, you would see an immense performance improvement. PT3 will automatically move the files by default (unless you changed the configuration), but for FTP the client needs to be completely closed down first as FTP locks the files and won't let us move them.