Are you in Factorio version 0.16? I think this is related to some changes I made for 0.17, but didn't properly mark those versions as being incompatible with 0.16.
Is there a reason you haven't upgraded to 0.17 yet? Its been out for months and works great. You just need to enable it under steam game properties, beta program. Otherwise, I'd suggest going to the download page and grabbing whistlestopfactories 0.1.9 which was the final version I released before 0.17 came out, so will work great with Factorio 0.16.