mikedehaan:
Any ideas why the Atmel route would not recognize the chip until Arduino wrote something to it?
Purely coincidence.
How do I initialize virgin chips?
No need. AVR processors come from the factory ready-to-run at 1 MHz. The Flash memory is filled with 0xFFFF which is an illegal opcode. Illegal opcodes are executed as NOPs (details here... http://support.atmel.com/bin/customer.exe?=&action=viewKbEntry&id=227 ). Apply power and the processor starts executing code that does nothing.
In other words, all you have to do to "initialize" the processor is upload a program.
The Arduino Uno as an ISP did something. I can't say what exactly, but once I configured the Arduino to be an ISP (uploaded the ArduinoISP sketch and changed some settings in the IDE),
Which settings?
I was able to deploy to my test ATTiny44. To test my deployment, however, I hooked up an LED to one of the pins and got nothing (I deployed the blink sketch). I changed the blink program to turn multiple pins on and off just in case I got the wrong one on the board. Still nothing.
What board was selected when you uploaded?