Hi joe! I wouldn't worry just yet. To begin with you don't need to use C6; you can use any program that sends sysex. Sysex Librarian for OSX or MIDI-OX for Windows are both fine.
Next, I'd suggest re-doing the main firmware update before trying the panel again.
For the main firmware update, you power on the unit with Fine Tune and Filter Cutoff pots at minimum, and the Pitch Bend wheel held all the way up while you switch on the power. This puts the unit into bootloader mode and readies it for the main firmware update file.
Next (after powering on in bootloader mode) open your sysex sending software and select the Sub 37 as your MIDI output device. You mentioned it sometimes not being recognized, but it should be if you power up in bootloader mode, connect USB, and then open the software.
Once you get this far, send the main firmware sysex file. You should see the red MIDI LED blinking on and off the whole time the file is being transferred. One possible advantage of Sysex Librarian is an accurate progress bar that definitely tells you if the file is still sending or has finished.
After the main firmware file has definitely finished sending, the unit should be in a state where you can send the panel erase, then the panel firmware.
Yes the panel erase is nearly instant; all you should see is a tiny blip or "hitch" in the blinking of the Arpeggiator Rate LED. I would recommend to wait 5 seconds after sending the panel erase, before sending the panel firmware. In a normal update, there is a message on the LCD for that 5 second period which tells you to wait until the screen goes blank, and then send the panel update file.
(edit: I experimented more with this today, and in the case where the panel is already blank/all LEDs lit, I don't think you actually have to wait between sending the erase and sending the panel firmware. Seemed to work OK sending them one right after the other)
So, finally, send the panel update file. Again you should see the red MIDI LED blinking on and off the whole time the file is being sent. If the pattern of the blinking changes, so that both the Arpeggiator LED and the MIDI LED are blinking in sync (both on/off at exactly the same time) this indicates a transfer error... if this or anything else unexpected happens please email me directly (my name at moogmusic.com). Otherwise, once the panel firmware file is finished sending this time, the unit should reboot to the new firmware and there will be joy throughout the land.
Please let me/us know how it goes. I'm very sorry for the trouble!
We'll be sure to put a more friendly firmware-update interface into the Sub37 Editor, which is currently in development.
All the best,
Amos