Ok, so although the video out of the 5D Mark II is standard HD and encapsulated into a .mov file, Adobe Premiere Elements does not have the codecs, sorry for stating the opposite, I thought it did.
I found a thread that might be helpful:http://www.flickr.com/groups/canoneos5dmarkii/discuss/72157616483148388/
Check the answer by rgphoto70
, he gives a pretty nice solution. On my PC I have not noticed any of the flickering problems they mention, I do have a pretty powerful graphic card with 1GB of RAM though.