If you don't have a batter the RTC is probably not functioning correctly. It won't operate without SOMETHING there. If you want to run it without a battery, put a bit of bare wire or something else conductive in the battery holder to short out the leads. Most of the time they'll run like this (though of course you'll loose memory when it loses power).
pandimus, that's the way the battery clip is designed to operate. I used that clip as a holdover from when I designed the Hydra. On that design there were other components/pads UNDER the battery so we needed it raised up. On this design that isn't the case. In version 2 of the Typhon I'm using a different clip, fwiw.
Speaking of version two, what do people think about the FTDI chip being onboard? It would mean you would not need a separate FTDI breakout to program the device, but it would bump the price up by ~$5. Right now, I'm thinking I may put the parts in the design, along with a header for the serial port (as there is now) which would let people choose. If you wanted it onboard, buy the parts and solder them in. If you already have a cable or BUB or other breakout, leave the parts off and just plug your breakout into the header. What do people think of this?