Hello,
Probably the mod load order or something about data load stage is changed, I'll take a look.
Thanks for the bug report and thanks again for the kind words!
Update: Yes, I found the reason, I'll send a fix ASAP.
Update 2: If you are curious about why that happened, take a look at "%Appdata%/Factorio/factorio-current.log" file. If you are playing with mods, this file is really helpful.