Sorry - looks like I posted the end of a rant. Here's the problem:
I want to simultaneously record an EXS24 bass with my left hand and an EVP88 piano with my right.
check "Auto demix by channel...." in the "Settings/Recording/MIDI" page
set each track to its correct MIDI channel
arm both tracks to record
select track 1 or 2 in the arrangement window
record the two tracks, playing both hands together on the downbeat
The first note played on the un-selected track is always delayed noticeably, throwing my playing off. I have a couple of midi keyboards - they both do this. The only workaround I've found is to start the count-in a bar early and play a note with each hand to be thrown away.
I'm using the latest version of Logic Pro 9 with an Apogee Duet.