Please make life easier for us, firstly please stop these sort of comments like "What gives??!!??" and "Why is it that I feel like I am paying to be a beta tester for this product??!!??" "Man, the more I use X3, the more issues I have with it and reminders of how poor X2 was for me. IF I found one good thing for 3 bad things I find, I would be happy, maybe." This is just a snapshot of what I've written today. You are perfectly entitled to your opinion, and maybe your opinion is right, but please don't expect everybody to rush to your forum thread. I would encourage more positivity and be more business-like about it. Right now you are putting up barrier before we even get to help you (we are not Cakewalk), I just got about of bed to read all this and now I'm depressed.
Secondly I apologise what I wrote just now, please don't think it's personal I've felt like that myself sometimes and I say things like this occasionally. Thirdly, moving on...
Please could you give us full steps to reproduce in test case format, here is an example.... this makes things totally clear.... If you have issues this is the perfect way to get your point across, it will actually help people get it the root of the issue. You should always start with a brand new project.
Example
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STEPS
Turn on 3 USB MIDI devices (such as keyboards), each MIDI device has it's own channel (say 1 + 2 + 3).
Start Sonar X3D
Create new project
Insert 3 Dimension Pro softsynths.
Assign an exclusive sound for each softsynth.
Assign a single MIDI device to each softsynth track, making sure the MIDI input channel is specifically set correctly. i.e. If it's a Yamaha keyboard on channel 1, assign Yamaha Keyboard -> MIDI ch.1.
Check to see if instruments play correctly.
Save the Project.
Close Sonar X3D application.
Turn off one MIDI device.
Start Sonar X3D
Open existing project.
Now play the MIDI controllers.
EXPECTED...a) Some warning that MIDI devices have disappeared.
b) All three MIDI tracks have maintained their values, however the missing device is flagged up in some way.
ACTUAL...The track with the missing MIDI device seems to have had the MIDI input changed to one of the other MIDI Input devices (which is weird).
Another MIDI Controller will have it's value changed for no reason whatsoever.
A third MIDI Controller will have the value persist.
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Thanks and sorry to be so forward.....