I've got the same device (well V1.0) so trying to remember. Once flashed, it's in 'flashed mode' or normal mode [ready for the console - it should light up red], and when inserted into PC, it's recognized as an usb hub.
You'll need to enter into debug mode again. On Version 1, it was pressing one of the buttons and then (while first button still held) press and hold the second, release first to get into debug mode - therefore able to flash the Maximus device.
Also I noticed that once I flashed the device, if I didn't 'Start Application' [on the FLIP software], the device was still in flash/debug mode and the LEDs wouldn't light up. I needed to get it out of flash/debug mode - if that makes sense.
Also some hex file might not work for that device. The ones that Evilsperm compiled seem to work really well for my Maximus. Note that I was able to flash, erase, test many times without destroying the device. Err meaning that it doesn't seem to be like an Xbox360 DVD Rom, when flashing with the wrong firmware could brick the DVDRom, these devices seem to handle most hex files. Though choosing the correct one is better lol
Hope this helps. In any case, try hermes v3 again. If that worked originally, then it should work again. Oh yes, I gather that updating is what you want, but it's at least a test to see if the v4 is faulty or corrupt or something else.