Welcome to the board! It looks like you posted your question right before the server went down, rotten luck, but everything should be running much better from now on! yay. Anyway, welcome to the world of pigs.
I would think, that if they where believed to be a bonded pair before who got along well, that after they get used to their new surroundings, they will again. Mounting is very common, even between males (if you are absolutely sure they are males??) however a move may spur a fresh "you need to remember I am in charge" from the more dominant pig. I would let them work it out on their own, I doubt separating them will be necessary.
What sort of cage do you have them in? Smaller cages can however exacerbate this sort of behaviour, basically, if you had to live out the rest of your days with someone in a bathroom, you would want to be the person making all the decisions right? As if the other person does things you don't like, you can't get away from them.
I would recommend a trip to
www.cavyspirit.com and visit the pages on socialization
www.guinealynx.info (for the care guide primarily, although the whole site and forum are excellent, and the medical information cannot be beat!)
And please visit the common misconceptions thread posted in Cavy Chat, it has tons of great info too!