This is a known bug. One thing you can try is upgrading to the newest version of xdotool. If that doesn't work, then check out this page, especially answer #29:
http://code.google.com/p/semicomplete/issues/detail?id=13
The issue was resolved by this pull request on 2014-04-07 (which is more than 3 years ago now). If anybody is still having this issue today, I think your best bet is upgrading xdotool.