Hey Simon,
I'm sorry for your frustration. I promise I read your entire post, but I did choose to try and focus on where I thought your issues were. I'd like to focus on your current stumbling block to try and get you developing then I can look further into these other things.
1) Using the GUI for the TRF7960EVM Rev A is described starting on page 22 of the Users Guide: http://www.ti.com/lit/ug/slou192c/slou192c.pdf
2) I actually don't know what the 0xA0 command was there for. I believe it was remaining for the TRF7960 EVM hardware, which has be obsolete for about 2-3 years but some people still have. I'll try to go back to the TRF7960 code later and confirm this theory. It shouldn't have interferred with your Com, but it deffinantly won't since you removed it from the GUI.
3) I am able to program the EVM with both IAR and FET-Pro430 from Elprotronic. I also did a memory read as you did, attached incase you wanted to see it. I'm running 64 bit Win 7. I'm using IAR version 5.51.6 for MSP430 in the default spibiwire mode. I just downloaded the latest FET-Pro430 from Elprotronic, version CS014X01.
Since you have tried 2 different programs to try and download code on multiple boards and even a new chip, I'm suspicious that your MSP-FET430UIF may not be behaving correctly. When I switch back and forth from FET-Pro430 and IAR, it keeps promting me to update my FET tool firmware. (the programs just use 2 different versions of this firmware).
Are you getting these prompts as well?
Do you have any other MSP-FET430UIF's to try and program these boards with?
Do you have any other TI EVM's you could try the FET430UIF with?
Here is a wiki article the helps address many possible FET430 tool issues: http://processors.wiki.ti.com/index.php/MSP-FET430UIF#MSP-FET430UIF_Troubleshooting
Below is a screen capture of my FET-Pro430 setup and settings for your reference.
Thanks,
JD