Plus, it stays on equihash the entire time, with no indication it is also switching or thinking about also switching. Now, this is an all NVIDIA rig (4 1080ti, 2 1080), so equihash is likely the most profitable at any given time. How can I be sure that A) its running/switching correctly and B) achieve the same stability as a pure command line start?
Equihash is usually the most profitable algo for NVidia 1080 Ti.
In spite of this, your script should change from time to time to other algos. You can check on the home page of MPH which one of them is currently the most profitable for your graphic cards. Your script should in principle follow that trend.
It's hard to be sure what your problem exactly is, but I would say that something is wrong with the switching script on your side. Also, mind that the ports are different when you mine a single coin, single algo, or mutliple algos.