A minor issue with the latest update.  I have 2 LBC docks running (on 2 monitors, but that may not be relevant), with one docked and one undocked.  If I open/close the Prefs window or close/reopen LBC, the undocked one automatically docks, i.e. forgets its previous undocked status.  The beta version you posted at
https://www.donationcoder.com/forum/index.php?topic=26398.25 on 11/18, which has the same version number as the one here, doesn't have this issue and remembers the docking status.  So I've switched back to that one.

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!!)

Having borders enabled or not, once you close prefs or restart the program the docks will end up on the same monitor.  (Which monitor they both end up on varies, and it's not clear to me what determines the choice of the lucky monitor each time.)  Can you recreate this issue on your system?  As I mentioned before, I can circumvent the issue by running 2 instances of the program.  Is there a way to have the 2 instances run by default at startup?