You are running bridged 32-bit plugins in Reaper x64? You should try 3.12rc
http://forum.cockos.com/showthread.php?t=43676 (
http://forum.cockos.com/showthread.php?t=22836), the latest build has some significant x64 bridging improvements.
When you say you don't have this problem in Cubase, you are talking about the same setup, Cubase x64 running 32-bit plugins in a VST bridge?