Media 100 Suite v1.7 was released last week. Among other things, it fixed a longstanding bug in the "Stereo Mix" audio export option.
Unfortunately, the fix for that problem caused a different problem in the other option, "Buses as Separate Tracks."
There is no effective workaround. We're working on an update which we'll get to you as soon as possible. If you must use the separate buses for your workflow, I recommend that you reinstall the previous version.