Okay guys, i think i have fixed the problem. (touch wood)
Im not exactly sure what it was, but i'm going to give a few suggestions anyway to make me sound smart.
First off i wiped the hard drive, reinstalled windows etc. and then mach wouldnt link with my machine atall,
even though i set it all up. So i put mach3 onto an external drive and then loaded machmill from that, all the settings were already there, and hey presto, machine jogged as it did before, and now the rapid speed is back to normal.
But now i'm back in square one because i need to do it again with another computer which has the same problems. I think i might have a dodgy serial lead or even a dodgy driver, so i think i'm going to get new ones to go with my new build. But anything is better than having another unproductive day and spending 8 and a half hours trying to fix software.
Thank you all alot for helping me!
You never know I might be able to help someone someday lol.
Gaz.