Hello-
Both the console and remote software are wrapped into the same .zip file on the website:
http://www.etcconnect.com/docs/docs_downloads/console/Express_3_1_Software.zip
e2.bin is the console software, and will upgrade the desk to 3.1 (which you've already done). run.bin is the remote unit software, and that will allow you to upgrade the remotes - you've done this process with the older software, so it should be easy.
I can't recall what the monitors show or what the LEDs should do off the top of my head, but try the latest software and if there are problems, call in to technical support. If you're a Badger fan, the closest support is almost certainly Middleton: +1 608 831 4116.
Heh, *that*'s what the other file is for! I'll give that a whirl and see if it fixes the problem (and yes, my closest support is definitely Middleton, although I'm in Minneapolis so there are a few local dealers as well).
Thanks!
--Forest
www.etcconnect.com