That's because the 9300 and the 9600 have different IR processing engines. The 9600 and the 9800 support more IR code formats than the 9300/9400 IIRC.

I know from past experience that the TSU firmware.exe extracts the image to a temp folder and all the files are read-only at this point. When you exit the program, this folder is removed.

As you seem to be looking inside the 9300 with putty or some other tool, I'm curious as to how you got to connect to the 9300 console. Or by chance did you just mount one of the jffs files from the image?