The command Send to MIDI > Used Instruments MIDI Settings sends sometimes wrong program changes. In fact program changes are duplicated between MIDI tracks.
example: assign MIDI track 1 with program change 1 (program button checked in the instrument's parameter box in arrange window), MIDI track 2 with program 2, MIDI track 3 with program 3 etc... After several commands Send to MIDI > Used Instruments MIDI Setting, track 2 send program 1, track 3 sends program 1, track 4 program 3, it's random.
To reproduce this bug: Assign a key command to Send to MIDI > Used Instruments MIDI Setting, create a multi instrument in the environment window, create a monitor object, link the output of the multi instrument to the monitor, create MIDI tracks in the arrange window, create sequences on each track, assign different programs on each tracks (program button checked) and perform the key command Send to MIDI Used instruments several times, take a look to the MIDI monitor and see the chaos.

This was allready sent to APPLE several times, but without result. maybe we should scream harder...

Thus: Anybody who recognizes this, send a report to
http://www.apple.com/feedback/logic.html

They must do something about it. It can't be that hard?

I REALLY UNDERSTAND YOUR PROBLEM BECAUSE I JUST WROTE ABOUT IT IN THE FORUM, BECAUSE I USE MACHFIVE OR KONTAKT SAMPLERS... AND I TRY TO RESOLVE THIS BUG FOR A LONG TIME, WRITING, READING, SEARCHING ON THE WEB FORUMS... ETC... BUT NOBODY CAN ANSWEAR ME. I JUST HAD A WORD ABOUT IT AT THE APPLE EXPO IN PARIS : "IT'S NOT THE PHILOSOPY OF LOGIC !!!"
IT'S INCREDIBLE. THIS BUG IS FROM THE BEGINNING !

Strange...
I don't have similar problems with my Logic 7.1.1 - MAC G5 dual 2 GHZ, Unitor 8 mk II MIDi interface..

Everything with program changes works O.K. - but I am not working with Multi instruments, I am creating instruments in environment window one by one, every instrument separately, using >define custom bank select messages< and adding bank and program numbers in arrange window - NEVER experienced problem. Maybe non-existing bank select commands ( cc0 and cc32 ) cause this?
If you are using hardware MIDI synths and samplers, read carefully owners manual with program change messages,
and bank select and program change numbers, and ALWAYS CREATE NEW INSTRUMENT in arrange window, do not use "ready" tracks from arrange window, maybe your "autoload" song is some way "corrupted"
All the best,
slowstar