thanks for the thorough tests and for reporting it all!
So it seems to me that we have some kind of a work-around: load the project file (or start the BomeBox) without the USB devices attached. Then, when fully loaded (project file is highlighted on MT web config page), attach the USB devices. In general, don't touch the BomeBox during load time of the project file...
I believe that you will not need to do a factory reset when experiencing problems. Waiting until the load process is done, and/or power cycling should reset it enough.
The "load native settings" error is inconvenient, but it fully recovered using backup settings. The 'Gateway error' seemed to be a problem with the internal web server of the BomeBox. Maybe the CPU was 100% busy with loading the project file, blocking the web server from responding? I could not reproduce this behavior. If you have that again, let us know.
Last, but not least, you wrote:
I connected usb power to Bomebox through usb power-meter and when I powered on Bomebox without usb hub connected, it shows about 4.80V / 0.26A, but as soon as I connect usb hub with all devices powered on, the power-meter shows about 4.98V / 0.15A, but all is working fine.
If I understand correctly, you measured the voltage going into the BomeBox using the micro-USB connector? Then, the voltage depends on the power supply you're using. Our experience is that most USB power supplies have bad voltage stabilization. They are meant for charging, and there, a stable voltage is not important. Typical behavior is that the more current is drawn, the lower the voltage. And when current changes, voltage will temporarily jump up or down. The BomeBox can handle lower voltages (its CPU uses 3.3V), but jumping voltage can be a problem. And lower input voltage is a problem for powering devices on the USB host port -- but you're using a powered hub, so no problem there.
We have not seen an effect on the input voltage when connecting a powered USB hub. Although some (bad) USB hubs feed power back to the USB host, the BomeBox has some protection against that. Maybe it was that when you connected the USB hub, the BomeBox was done loading the project file and therefore used less current, so that the USB power supply increased voltage?
Let's see if the PoE power supply helps.
Thanks for giving us new challenges for future firmware (and hardware) updates!