Notes on wrong side of stem in triads

[DJF]

I’ve used Lilypond extensively—especially for organ music—and have never seen noteheads in a chord appear on the wrong side of the stem. Unfortunately, I can’t reproduce the enclosed problem in a minimal example because the same code works fine in a file by itself. This is in the left hand of an organ part, and I’m using 2.19.39, though I tried it with the latest version as well with the same result. However, the chords look fine with 2.18, but using that version that isn’t an option because it creates many other (and more significant) issues. If I put the stem direction up, the chords also look fine … but, of course, they all need to be stems down. This was also happening in one right-hand chord in a subsequent bar, but ultimately I changed that chord slightly and it’s no longer an issue there. This only seems to happen with (some) triads …

I’m using a choir & organ template generated from within Frescobaldi … this happens no where else in the 86-bar piece, and no errors are generated when compiling.

The code for the example is below, but, like I said, it works just fine out of the context of my piece: 

<g bes d>8 <g bes d>16 <f a! c> <g bes d>8[ <a c e>] <g bes d> <a c e>

Any thoughts?

—

Dan