The ascent autopilot refuses to automatically dump empty stage, maybe a problem with sepratrons.

Can you stick a .craft file for a ship that demonstrates this problem on http://pastebin.com/ and post it here?

Can you simplify your craft so that the problem still occurs with no mods installed (other than MJ2)?

Here you are: http://www.mediafire.com/?3bwdvzflbmwi0v7

It uses KSPX and ORDA but only for a launch escape tower and 2 OMS-engines:
http://www.mediafire.com/?cfjcpcjw73r2cad

Oh sorry, it just works fine, it just takes forever to actually perform the stuff