Hi Mark. Is the one that it's not working is in bex format, and the one that is working is in a different format? I wonder if it doesn't work with bex cubes? Problem Event Name: BEX64
We recently fixed an addfiletoextract problem that sounds like it could be the same thing. The Issue ID (for the upcoming release notes) is 791525. You can contact support for more assistance.
I'm not 100% sure what a bex format is although both files are text documents. The other odd thing is that I can add the file through desktop, but for obvious reasons I don't want to do that regularly.
Turns out this issue has to do with a calculated field being tied to a parameter within the extract. After rebuilding the extract and changing everything over to that new extract (not just simply replacing the data source...yes, this was really fun), all of my commands now work as expected.
Just wanted to share for anyone who was interested...