As far as I can tell, the beta has fixed the docks-remembering-their-respective-monitors issue. Now, upon closing Prefs or restarting LBC, docks appear on their last-assigned monitors and don't crowd on one. As for the minimizing to system tray, I hadn't used it much previously, so don't recall how it was behaving before. But with the beta, right clicking on the sys tray icon and toggling "Restore from Tray" only toggles between dock & undock; "Restore from Tray" seems to act the same as "Toggle Docking" for a given dock.
I should point out another issue I'd notice earlier, as well. If I have 2 docks running and I assign a transparent background to one dock and a colored background to the other, depending on which one is the colored one, they both appear w/ colored backgrounds. It seems to be determined by which dock was started first, but I'm not sure. So if dock1 is given colored bkgd & dock2 transparent, then that's how they appear. But switch the choice of colored & transparent bkgds for the 2 docks, and both appear w/ colored bkgd! (So the colored gene is dominant & the transparent one recessive, only if the right sibling is assigned the colored gene!!)