For those interested there is some more information about this topic.
First the mega644pa in my Wiring S board seems to have a fault.
I used the WinAvr Programmers Notepad for the testing as this quite a good C++ interface and has no issues that might be a problem in either the Arduino or Wiring IDEs.
If you need a good tutorial about how to start off with Programmers Notepad lookup www.newbiehack - some basic videos on how to program and set up AVRs.
The good thing about Programmers Notepad is that you can setup and test just about any Atmel AVR controllers- 8 to 16 bit. Not sure if it does 32 bit, but it handles mega and xmega chips.
Avrdude replied that device signature was different from that expected - it was close, only one hex character different, but not close enough.
So I used one of my 328p chips in the Eleven board to test the problem.
Avrdude replied with a success in the CLI.
The code was: Avrdude -c usbtinyisp -p m328p
And the chip initialization passed.
So the 644pa has some type of internal fault associated with ICSP.
Arduino has replied to me that only their boards are available and they don't seem to have any plans to open it up for all and any AVRs, for this you might need to use Programmers Notepad, but it is pure C++ based not Arduino speak.
However the Programmers Notepad is a good place to learn about C++ programming, how the device Port system works and allows the user to really get into some powerful C++ features.
I would suggest to use both IDEs and even try Atmels Studio 6 which has a lot of usefull information about all the devices including fuse data.
I think that finishes this thread for me, good luck.