Yoshimi LV2 patches not restoring

I've been using yoshimi as an LV2 plugin successfully for the last couple of years but have run into a problem this week - the patch settings are not restoring correctly when I use my standard template. The attached qtzs both have the first 3 tracks set to Bass/Bass 1, Bass/Bass 2 and Bass/Bass 3 (analog), as you can see in the qts's. However, they behave differently.

Test_YoshRestore.qtz
This was created from a bare file and restores correctly.

Test_YoshRestoreTemplate.qtz
This uses my standard template. On loading, only Track 1's patch restores; both Track 2 and Track 3 default to arpeggio1, the first patch in the list (your version of yoshimi may have different patches though).

Is something in my template causing a conflict? I've been trying to track down the cause of this (creating new yoshimi instances, as opposed to dragging/dropping between tracks; using different MIDI channels (have had problems with other LV2 plugins previously); resetting yoshimi's default patch directory etc.) but it seems to be something in the template. I've been using various versions of the template for a long time with no such problems.

I'm running Qtractor 0.8.0 (though the problem happened on versions from a couple of weeks ago) and Yoshimi 1.3.9M (which has been fine up until this week).

Thanks as ever.