Thanks for the report; as you might know, I get no notifications about discussions here. If you report any issues on the github issue tracker, I get an email notification of the problem, as well as a prompt when I log in.
Ill take a look at this one tonight and see if I can get to the bottom of it.
EDIT: Having had a look at it, this is Factorio preventing a part of how Treefarm worked in 0.12. Should hopefully be sorted soon - in the mean time, certain mods are going to be incompatible with Treefarm.