I am currently working on a web-site which is having two link, one local and the other international(.com). i am working with the same KWs on both of them. but i was amazed to find that though the .co. one is having a high ranking/positon (almost 4th, 8th and 9th with different KWs) the .com one is not to be seen anywhere !!!!!!!
Does the .com have any backlinks? I've found that you need a good number of backlinks (especially relating to the product) in order to get a good listing in Google and get a good PR.
Do a link:<domain name> on Google for each and compare where your backlinks are coming from.