Yes, it would be good to isolate whether this happens stand-alone, or only when in combination with LB/BB.
Regarding the "." key, there are a few things to keep in mind. If your arcadeEIP.ini file is in its default state, then the period is assigned as both the "magic_key" and the "exit_key". So assuming kiosk_mode=0 (the default), then the operation is that a short press of the period key will exit, and a long press (by default, 2 seconds) will show the menu (or to reverse this, you would set kiosk_mode=1). This ability to use one button for two functions is achieved using a hardware strobe, so it requires a real keyboard or a hardware board acting as one (such as an ipac) to work. It will not work using the hotkeys sent by the Stream Deck, unfortunately.
The good news though is that this should only be an issue if you wanted to, say, exit a game using a button on the Stream Deck rather than using your control panel (or keyboard). If you want to do this, one way is to assign the magic_key to a value that isn't used, like magic_key=? (or alternately, assign the exit_key to a value different than the magic_key). Doing this will effectively disable the "magic key" function, and revert to strictly discrete key operation (for example, " . " to exit and " ' " to display the menu), and both of these should now work with the Stream Deck's hotkey macro.
If you really wanted to have both a discrete exit function that worked with the Stream Deck, while also preserving the magic_key function for your control panel, let me know and I could consider adding an independent discrete exit key.
[Edit] I just went ahead and added a new discrete quit_key setting to arcadeEIP.ini. If you download the newest version (0.3.3.3) and just replace the executables and add quit_key=~ to the [Key Map] section, you should now be able to program a Stream Deck hotkey button as "~" to exit without messing with the magic_key/exit_key functionality (so you can probably mostly ignore the information above if you want). I'm not sure if that's what you were looking for, but it seemed like a good thing to add regardless.