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Dang. This has happened to me several times, and I too keep forgetting what the fix is!
Fortunately, I had the sense to make some notes, which I've managed to find:
Problem:
Mac (and DP) think MIDI interface is a 2nd MOTU MIDI Express XT.
AM setup and C'works call it "MOTU MIDI Express XT #2"
I've had this problem a bit with OS 9, but only once on X.
I'd just installed new MIDI drivers (MOTU 1.3), which may be responsible.
After much hooha involving file deletion, AM setup, C'works etc with no success, I went the "whole hog" and it worked!
Solution 1 (The whole hog) :
1. Remove all MIDI drivers except MOTU.
2. Remove C'works and AM prefs in main folder and in "By Host" folder.
3. Replace AM configs with older copies.
4. Uninstall MOTU 1.3 driver.
5. Restart with MIDI interface turned off.
6. Install MOTU 1.2.4d2 driver.
7. Restart with MIDI interface still turned off.
8. Open AM setup and select configuration.
9. Turn MIDI Express XT on.
10. Celebrate!
Or
Solution 2 (Just a pork-chop): (Discovered Later)
1. Open AM Setup.
2. Drag "MIDI Express XT #2" to line up with "MIDI Express XT".
3. Drag new cables to "MIDI Express XT #2", mirroring the existing connections.
4. Delete "MIDI Express XT".
5. Rename "MIDI Express XT #2" as "MIDI Express XT".
6. Back up configuration.
7, 8, 9, and 10. Celebrate!
If "solution 2" needs frequent repeating, which it seems it does for you, I'd go "solution 1".
Of course, my driver numbers are out of date here; I'd go for the latest as a matter of course.
Oh, and be sure to follow "solution 1, point 2" to the letter.
I avoided switching the XT on until the last possible moment for fear it'd make another appear in AM setup.
This had happened before, I believe, although I can't repeat it.
Hope this bears fruit, Sergievsky.
