A bit more investigation has shown further where the problem is. It appears there are actually two issues.
The first is specific to EJS files, when the build completely fails (only outputs the first "building" message) it is because the XMLHTTP call to get an EJS fails in some way.
The second issue is when one of our build.html pages steals one of our other apps to include it. Sometimes that steal fails in some way and therefore fails to include the other app (though the rest of the build works).
We have a work around for the EJS files, we have just stopped stealing them and the build then works. Or at least I assume that is a valid work round, I need to check that the EJS files still work when just included along with our production.js in the right folders.