http://www.cockos.com/forum/showthread.php?t=12690
Im using beta 2 of course, and it seems like on some renders reaper puts a gap of silence of differing lengths towards the end of the render.
some plugs that i am using at this time are
reaEQ
MAgix - Amphibia
Voxengo - HarmoniEQ
reagate
...
its a random occurance but limiting to realtime works.