I'm working on it right now. Essentially its an issue with having fewer coins actively being mined (just because there are fewer profitable in the last day or so). If we start on litecoin, switch to doge, and go back to lite before a block has been found, we end up with some duplicate shares. I'm working on a patch right now, not sure on ETA though. Has nothing to do with EU vs other servers, should be across the board.
I noticed my daily avg hashrate had dropped quite a bit, despite being steady +/- 100-200 khash for over a week. Is this why? Sorry, this is a hobby for me I don't particularly check my miners much.. ever.. so long as they're on and running according to will's page lol. I use the USEast not EU stratum though..