All my MIDI are transposed 1 semitone!

Have you looked to your transpose/global track (up top in the timeline)?

Jules,
I experienced the same problem. But mine was a lot worse.
Do what Justin says and go into
VIEW > Global Track Components > Transposition and...
BE CAREFUL...my problem stemmed from that transposition track destructively applying changes to the notes.
Put the automation line in that track at 0 and you should be fine.
(It could also be a transpose applied in the parameters of the track).

Are your instruments transposed? Is your sample rate correct?

Hey Jules,

This exact same thing has happened to me at least 3 times now, only my notes were about an octave higher (everything sounded like chipmunks, and the sample rate wasn't changed). Double checking everything as you have done revealed no change in the song whatsoever (and these were pretty large sessions with a lot of work being done). I've yet to figure out what caused this to happen - finally ended up having to do the entire sessions over from scratch. It's extremely frustrating to lose all of your work like that - please keep us posted if you happen to find out what caused this to happen.

Is the problem coming from Midi or Audio or both?

Answering this will help us help you!

Thats happened to me a long time ago. Somtimes if you're using a keyboard with key transposition or an old keyboard, it faulters. If you change it then go in score window then go out of it . It gets hung up. Somtimes if you return your studio to normal setting and boot up again , all is well. The problem comes from your keyboard.

What kind of keyboard are you using just in case?
And did you use the transposition from it? just in case.
It could be unitor interface. i've heard amt8 are very reliable.
Do you have midi pedals attached ? they tend to grab midi with logic and run with it.
It could be your AUTOLOAD is corrupt. try creating a new one or compare by process of illimination. Or let it create a new one for you. Or try a standard midi file.
disconnect midi cables and connect again.

Again, an old simple keyboard can cause havoc in midi. I have one, and I still use it because it works for me on other issues.

FYI, I am pretty conscious about things and familiar with Logic and I have experienced this one, AFAIK no fault of my own. It makes you go crazy-why is my drum sequence all whack? I returned to it (after quitting and it was gone, this is very rare in my experience but I did check everything and simply quitting worked to fix it. Cheers.

This has bugged me for ages. Thanks to the advice here I've set the Global Transposition track to Zero. Will see how much difference that makes to songs. Very hard to analyze something that only happens occasionally!

I had this once, it was happening on every song. Trashing the prefs fixed it for me, I have no idea why.

if it happens all the time, couldn't you copy the track, then drag the MIDI info onto the new track? (works in GB)

I've had this a few times. Absolutely nothing can be done in the session to fix it (not a transposition problem). I have to reboot (just restarting logic isn't enough). Once I'm freshly booted, the problem is gone.

There's no predicting it - a song I've opened dozens of times simply goes wacko once, after reboot, no more transposed midi!