I don't recommend PJ64 running on that system, especially beacause it only has got 56 mb ram. I think you should try other emulators like 1964 or ultrahle 2064, but PJ64 is your choice. Okay, ontopic. PJ64 1.5 final is a little slower than beta, that's known. How much fps did you have in the beta-version?
Edit: my post was before the one from MisterFriday, but there is a timing-problem again, so the posts might be in the wrong order.