Yes.

Directly to the device with MMA installed?

I synced with MMW via USB.

How did you sync? If you didn't do MMW > MMA then yes, you're relying on Android Media Scanner instead of MMW settings tags in MMA.

Could it be because of the filename, i.e. 1-01-Reflektor.m4a?

Odd, I can't reproduce, it shows Track# without any Disc# info here.

No, here are the properties of the first song in MMW:

Are you sure you don't have the files tagged that way?

Like this:

Where do you see this?

Tracks on multi-disc albums are displayed as:

101. Disc 1 Track 1
102. Disc 1Track 2
103. Disc 1Track 3
...
201. Disc 2 Track 1
...

Would be better if they were displayed as:

1.01. Disc 1 Track 1
1.02. Disc 1 Track 2
...

or even better IMO:

1-01. Disc 1 Track 1
1-02. Disc 1 Track 2