I did change the 'board type' for the different frequency builds. I loaded a basic sketch into the different frequency boards and then looked at the disassembly in AVRstudio.
There are assumtions made about the clock frequency (either 8 or 16M), which is fair enough I suppose as thats what Arduino's run at. I'm not too bothered about it for now and if it gets to the stage where its a problem then I'll look at (trying) to do something about it.
I do use the basic libraries for Kicad, but each time I make a new component, I add it to my own library so it has grown over time.
I looked at going the Eagle way some years back but did not want to get locked into a system that was limited in the 'free' release. Kicad has no restrictions in that sense.
Its not as 'seamless' as Eagle, but its quirks are not such a handicap that I cant live with it.
I have not experienced the problem that you describe, but the releases are regular so whatever it was may not be there any more.
I think I have arrived at a 2nd build version now.
It has more flexible power options. Positions for two regulators on board, a 5V and a 3.3V.
With the two power rails on the board, the micro (and RS485 if fitted) can be run at 5V for full speed. The other items all run a 3.3V. The 5V rail can be connected to the 3.3V rail (with no 5V reg fitted) and the whole board run at 3.3V. Also now fitted,
A power LED
A LED on one of the I/O pins
A reset button
The radio connector is now the cheap nRF version as per ebay (and many other sources)
Ground-plane beneath the battery (for the RTC) is fixed and the 32Khz xtal footprint fixed.
The PCB is done, I just need to check it over for a few days and see if I spot anything wrong then I'll get a batch made.
Its 5mm wider so still well within the 50x50mm PCB area at Seedstudio (and others)
Since I'm ordering boards, I'll do a RFM12 adapter that fits onto the radio connector, I use both.
If it all works OK then I think that will do for me. I'll release the files and anyone can do what they will with it

Schematic now attached (you need to log-in to see it)