Hi there. I am running mothur on Ubuntu on Windows 10 and downloaded the file for install from the newest release github page (https://github.com/mothur/mothur/releases/tag/v1.44.3), but it does not seem to be version 1.44.3. If I recall, the version indicated when I ran it was mothur v.1.42. I also downloaded mothur from the newest release page onto my Mac using the OS file and was able to run through the entire MiSeq SOP with no issue.
PS I posted this as an issue on github, too.