Its very disheartening to have to post here for help as I really wanted to solve this problem on my own but to no avail.
I purchased some 328's from http://cgi.ebay.co.uk/Atmel-ATMEGA-328P-PU-UNO-bootloader-XTAL-22pf-caps-/320702036687?_trksid=p5197.m7&_trkparms=algo%3DLVI%26itu%3DUCI%26otn%3D5%26po%3DLVI%26ps%3D63%26clkid%3D271121225359777888
and a SparkFun FT232R breakout board (removing the solder jumper so as to go from 3.3v to 5v, also checked voltage with my meter). I followed the instructions at http://www.arduino.cc/en/Main/Standalone
(I think there is a problem there because at one point it says to take VCCIO to the +5v rail but the photo differs, I went from VCC instead which I believe is correct)
When I powered my 328 for the first time both the TX and RX leds on the breakout board flash simultaneously three times, the power led on my breadboard is on and the led on p13 goes into a loop of three led blinks but when I try to upload a sketch things are not working.
I hit upload in the IDE and as soon as compilation is complete I hit the reset button on the breadboard (have also tried different combinations/timings of this), the TX led on the breakout board flashes three times, then a long pause, then a single flash of the TX led, another pause then the IDE responds:
avrdude: stk500_getsync(): not in sync: resp=0x00
avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x51
I tried two different 328's with the same result. They came preloaded with the uno bootloader but to be sure and validate the chip I took one of them and placed it into my UNO, uploaded a sketch to it no problem so the 328 itself is fine. I put that same 328 back into the breadboard and opened the serial console, I get my serial output back as one would expect. Try to upload a new sketch on the breadboard and again I get not in sync.
I've tried on two different 64bit win 7 machines (of which both work fine with my uno) I've also tried on debian squeeze. Tried different cables, different board selections in the IDE, Obviously I've checked the com port stuff and as mentioned I've got serial output coming back. I've rebuilt the circuit on the breadboard several times now, I've double checked my resistor values (as I have in the past put the wrong value resistors in place, doh!) I've tried changes to the baud rates in the boards.txt file and set the baud on the com port to match (assuming 8 bits, no parity no flow control is correct?), I've read many posts and now I am totally lost.
Is anyone able to help?
Thanks in advance.