Hi,
the reset thing with serial is done with a modified avrdude : GitHub - deanmao/avrdude-rpi: Fixing the lack of a DTR pin on the Raspberry Pi for the purposes of uploading hex files to the arduino
The atmega doesn't share the reset pin with SPI and serial, because I change the reset pin when I change the programming method : if I do a test using serial, I remove the SPI reset line and put the serial one instead.
When I try to upload the blink sketch the second time, I could see the LED blink twice fast, and then continues to blink normally, when the autoreset command is sent. So I'm assuming it's resetting normally ?
But I agree with you, this behaviour suggests there's a problem with autoreset (this is why I added some debug LEDs on D8 and on the reset line).
I just tried to use a known procedure (http://wiki.openenergymonitor.org/index.php?title=RFM12Pi_V2) but it's not working either : burning the special optiboot with fuse settings for 3.3v/8MHz doesn't allow serial programming (the SPI programming works well though).