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I assembled an EmonTx and an OpenKontrolGateway last week and spent the weekend with endless attempts to program the devices, searching multiple forums,... without success: 'stk500_getsync()' and 'stk500_recv(): programmer is not responding' messages.

Beside EmonTx and OKG, this is my environment:
- the SILabs CP2101 USB2UART programmer (bought together with the MC kits)
- Windows7 64bit, latest Silabs driver installed. Arduino IDE 1.0.1 shows Serial port: COM3 when programmer is connected.
- Ubuntu 12.10, Arduino IDE 1.0.1 installed from 'universe', USB access enabled for the user. Arduino IDE shows Serial port: /dev/ttyUSB0 when programmer is connected.
- 'Board' set to 'Arduino Uno' in both environments

When running 'Upload' this is what I get after compilation has completed:

On Ubuntu:

/usr/share/arduino/hardware/tools/avrdude -C/usr/share/arduino/hardware/tools/avrdude.conf -v -v -v -v -patmega328p -carduino -P/dev/ttyUSB0 -b115200 -D -Uflash:w:/tmp/build2305710485166878365.tmp/Blink.cpp.hex:i

avrdude: Version 5.11.1, compiled on Oct 30 2011 at 10:41:10
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/usr/share/arduino/hardware/tools/avrdude.conf"
         User configuration file is "/home/knut/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyUSB0
         Using Programmer              : arduino
         Overriding Baud Rate          : 115200
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500_recv(): programmer is not responding

avrdude done.  Thank you.

On Windows7:

D:\Program Files (x86)\arduino-1.0.1\hardware/tools/avr/bin/avrdude -CD:\Program Files (x86)\arduino-1.0.1\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega328p -carduino -P\\.\COM3 -b115200 -D -Uflash:w:C:\Users\knut\AppData\Local\Temp\build4614834237107931764.tmp\emonTx_CT123.cpp.hex:i

avrdude: Version 5.11, compiled on Sep  2 2011 at 19:38:36
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "D:\Program Files (x86)\arduino-1.0.1\hardware/tools/avr/etc/avrdude.conf"

         Using Port                    : \\.\COM3
         Using Programmer              : arduino
         Overriding Baud Rate          : 115200
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Recv:
avrdude: stk500_getsync(): not in sync: resp=0x00

avrdude done.  Thank you.

Yes, I checked similar 'stk500_getsync() threads' in this forum:
- the MC is plugged in the right direction
- the USB2UART programmer is plugged in the right direction
- the voltage check is ok
- on Ubuntu 'dmesg' and 'lsusb' are showing that the Silabs device is connected  

The ATMEGA328s are ok: when connecting an AVRISP MKII to the SPI/ISP, I can read the IDs, fuses, flash,... with Atmel Studio. I found a bunch of bytes written at the beginning and the end of the hex file, so I assume the bootloader is there.

Are there settings I missed? Baud rate? Anything else?

Since I am able to reproduce with 2 MC boards in 2 different environments, I guess it is indeed an issue with the USB to UART loader (see similar thread: http://openenergymonitor.org/emon/node/942)