I couldn't tell you why one worked and the other one didn't, other than which one worked for me.
Here is my experience:
When I was looking for the firmware, I came across two different instructions, this one and this one. I went with the latter since it had a later update date.
I downloaded and installed the firmware linked from the second webpage above. I should have known something was wrong because when I was poking around in the configuration.h I noticed it was already setup for a SD3. Both websites/instructions said the default setting should have been for a SD2. Everything went fine until I connected the printer in Repeater Host. No matter what I did, the temperature for the hotend was high. I knew something was right when I disconnected the lite6 thermistor completely from the controller board and Repeater Host was still reporting the high temperature.
At that point, I remembered the other website. So I went back to that website and downloaded the firmware that was listed and made the change to TEMP_SENSOR_0 and uploaded it to the controller board. I crossed my fingers and connected to the print with Repeater Host. BINGO, success!!! I finally got a low temperature reading with the Semitec 104GT2 thermistor connected. I should also point out the first firmware said beta whereas the second one I used didn't. Let me know if you need more information.