MIDI and Audio problems

1. The MIDI problem............the only way to explain this is by an example. I recorded something from my M-audio axiom keyboard, just something simple like a c major scale. Then i saved it reopened it then i played it back it now is a b major scale. If i open the matrix editor its still C but plays back in B and i must transpose it to make it normal. Never have i had this happen before. Has anyone else had this happen? How can i fix it?
Another MIDI problem is sometimes when i play back a MIDI performance it slows down and sounds like slow motion until it stops and says "sample rate 86672 recognized" i am at a loss on this one.
The Audio problem is simply that i get distortion in my recordings but none of my preamps clip. i can even have the gain half of what i would normally set it at, and it sounds distorted.
Any help would be great thanks
Mac Pro Mac OS X (10.4.8)

Possibilities...
There's a (now common) bug that causes bogus data to appear in the Global Transpose track, all by itself, and if the data that got entered was "transpose -1", then your C-major scale will indeed play back in B. To investigate whether this is the cause, open your Global Track display and see if there's any transpose data written in there. If so, delete it and see if that changes the situation for the better.
Another common thing to happen, that's not a Logic bug, is that pitchbend data might get "stuck" at wheel=down. If Logic isn't set up to reset PB (check your MIDI prefs), then the PB data won't be corrected, and will stay "low" util you reset it manually, i.e., flinging the PB wheel/level to reset it to zero. This is probably the best explanation for why Logic will seem to "repair" itself when you reboot/relaunch, because usually upon reboot/relaunch Logic sends out reset messages for things like PB.
As to the sample rate thing, I take it that you're recording at 96K? Or maybe 88.2? If so, you have a clocking problem somewhere.

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What?...
I'm sorry maybe I don't understand everything you are sayng... but I can replay to the titles of the Topic!
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you cannot use Punch-in on Fly when an Audio and instrument track is armed at the same time...
or better you can but the MIDI and audio output will be dropped for a moment
Provide a Logic feedback
http://www.apple.com/feedback/logicpro.html!
THIS IS A LOGIC 8 BUG!!! BIGGEST SERIOUS BUG!
I suggest you to use Logic 7 when you need that!
Thank you so much for remember me this..
I'm sorry no alternative solution... or.. if you have 2 Macs you can use one for Logic MIDI and another one for Logic Audio!
G

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I hope I'm missing something. when recording midi and
audio at the same time, with merge and replace turned
on, the midi is ok but the audio is NOT in replace.
Is there a way around that. If not does logic have a
play what's on top structure like nuendo? I need to
emulate a tape machine as closely as possible in this
application
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MIDI and Audio problems

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