RetroArch seems to load, run, and operate fine with just the '.' in place on the command line. As this is the command line that GameEx setup automatically for me (I am not skilled in such things) I left it as such, went to RA and installed the specific Cores which each command line noted, and went from there.
Updated GameEx, though it keeps asking to download and install with each restart. Ran, as an example, Atari 2600 > Adventure. Game loads, runs fine, exits as requested. Confirmed the Core is correct as the line requires. Then changed command line for Emulator Slot #1 (Atari 2600) to include drive letter. RA still working as it was with '.' in the command line, but command line now updated with drive letter.
Loss of Joystick functions still happens, somewhat randomly, after exiting RA and returning to the 'Play this Game' menu screen in GameEx. This does not effect Trackball nor Up/Down Spinner which can be used to navigate the menu.. but the Joystick and Buttons associated with it do not return until system is rebooted.
GameEx.ini log.txt runitgame.bat