Nothing like answering your own questions. Anyway, to contribute to future FLIRC users, here is a FAQ for headless FLIRC activities:
1) Shortcut custom hotkeys must be on the desktop to work.
2) Program your FLIRC with physical keyboard and monitor. Then carefully note below.
2) If using a headless PC, you CANNOT ever use RDP protocol to control/login to the PC if you want shortcut hotkeys to work. Shortcut hotkeys become disabled up on activating RDP and STAY disabled. Solution: enable automatic login and put your FLIRC controlled software in the "startup" folder. If you have to wade through prompts, program FLIRC with an "enter" key and hit that key a few times to bring up your software.
Arcane stuff, but maybe important to FLIRC users.