I'm afraid I can't really follow what you're doing and what the problem is here. Is the problem merely that a MIDI track you have is not included in your final mix? In this case please make sure that you're really routing it to a VST/software instrument, not just to the Microsoft "GS Wavetable Synth". I don't really understand the relevance of the guitar recording here, though. So maybe I misunderstand the issue. Maybe you can detail this issue a little more.
I now understand that you're referring to a VST effect plug-in that you're applying to your audio/guitar track, but I'm still somewhat baffled as far as the problem goes. The inclusion of the effect on your mixdown shouldn't require the locking of the track. That's a pure editing tool with no bearing on audio effect calculation and so on. Maybe this was just some intermittent problem or there was some other change in the program that caused the problem to appear and disappear again.
And yes, you're correct: Version 11 of Music Studio did still have the "Midi Studio" component, based on the old Logic sequencer. Version 12 was a completely new program, with audio and MIDI component being combined into one single application, all based on Samplitude code.
After installing the Atmos plug-in, you will find it under the "Synth" button in the button bar, which (by default) is located at the bottom of the Music Studio 12 screen. Make sure to enable the "Buttonbar" option in the "Window" menu of the program.
As far as your mixdown problem is concerned, I would probably also double-check the program settings in Music Studio (sound driver and buffer settings) and experiment a little with them. You could try to narrow down the issue. Press "Y" to bring up the audio system settings. Use ASIO drivers. Prefer the original drivers from the manufacturer of your sound hardware, but consider opting for the generic ASIO4ALL driver later. Start out with 16 bit / 44.1 kHz projects, even if your sound hardware can do better than that. Keep in mind that we're troubleshooting here. You can still use other settings later. The default buffer settings in Music Studio should be pretty safe:
ASIO buffer size under the ASIO Setup/Control Panel should be 512 for now.
At least I think these are all default settings. You could start out here and then experiment and adjust them according to your needs and sound hardware specs.
Well, maybe this helps and maybe you won't be coming across the problem again, anyway. I hope you can focus on making music, rather than troubleshooting. Would be glad to see the results in the "Show & discuss" section here some day. :-)