OK, I've figured this out. When you run the test suite from Maven, it
runs the custom.testsuitetest.java class instead of the .ats file.
It's all in the docs but I didn't understand that on the first couple
of passes. So in there you specify the order of your tests if you
want to run it from Maven, which by default simply scans the test
directory and runs them in the order it finds them (hence the
alphabetical order described above).
In short, your testsuite.ats file is only useful in CubicTest (or I
presume if you export to selenium HTML files) and has no relation or
bearing at all if you run the tests as Junit tests.
Hope that helps someone who had the same issue as me.
Teg