I’m also seeing this issue when using Honeycomb Bravo throttle bound to MSFS directly. Tested in Citation Longitude: the spoiler, throttle 1 and throttle 2 axes on the commercial twin-engine config (1st axis, 3rd axis, and fourth axis respectively). After hitting ‘ESC’ to see the menu and then returning to flight, my spoilers and both throttles moved themselves to 50%.
If I use spad.next to control the axes, I don’t get this problem – they do not reset.
Also, all my glass displays went black on the first exit/resume – perhaps because the avionics and power switches are on the Honeycomb Alpha. After switching back to using spad.next, I don’t get a glass display failure when exiting to the menu and resuming (I had to power-cycle the avionics to restore them before testing).
MS Store version (Premium Deluxe, all the fixin’s. Nothing in community folder. Navigraph Simlink and fs2ff connected to ForeFlight, as well as spad.next for input management, over SimConnect.)