On E9th, the 4th and 8th (E) strings should be tuned an octave apart rather than unison.
As for the 6th string 'acting up', keep in mind that that large of a guage in a plain (not wound) string is very susceptible to bar pressure and temperature changes.
I've toyed with the idea of installing a changer-finger that has it's axle-hole purposely drilled slightly off-center so that the 'top-dead-center' is causing the scale-lentht of the 6th-string to be ever-so-slightly longer than the rest of the strings to help alleviate that problem.
Somewhat similar as the 'compensated bridge' is on 'under-arm guitars'.
~Russ[This message was edited by Russ Wever on 08 June 2006 at 11:49 PM.]