A better way to phrase the issue: M should not be the same as L' R.

http://jsfiddle.net/AshleyF/2xAVX/106/

<h2>Repro</h2>

<h3>When I hold a cube like this:</h3>
<div class="roofpig"></div>

<h3>... and do an M move, it looks like this:</h3>
<div class="roofpig" data-config="alg=M | setupmoves=x">(x) M</div>

<h3>... not this:</h3>
<div class="roofpig" data-config="alg=M">M</div>

<h3>... which looks like L' R:</h3>
<div class="roofpig" data-config="alg=L' R">L' R</div>

Yes, setupmoves can reorient it, but that's a pain and adds complexity when displaying user-input or machine-generated algs; not just static diagrams.

I'm hitting this same issue I think.

<div class="roofpig" data-config="alg=M' U' M' | colored=UL UR">

This re-orients, and then colours the yellow sticks which are now at DL DR.

I think I can cure it, but I cannot determine whether it is causing any side effects.
Since the repo is not open, I can't make a pull request.
If you want to test my change, do this:
edit the roofpig and three js file
search for the string
this.map=t.start_map(),e&&this.track(e)
there is exactly one occurance.
delete the part after the comma, make it read
this.map=t.start_map()
Seems to me the fix is working fine.