The BIN file you list isn't in there.
The only one in there is:
RX-34_2007SE_3.2007.10-7_PR_COMBINED_MR0_ARM.bin
(note how the [1] is missing between the 3 and the .2)

And what exactly did 3.1 "fix" anyway?

Looks to me it's just a patch to sandbox in the development environment to bring it up to sync with the latest firmware release.