Thanks for the replies, I tried ../tools/configure and managed to get the files. Maybe I originally missed something in the cygwin setup.
Unfortunately with a new bootloader, mksamboot and OF 02.02.26, 02.03.31 and 02.03.33 I still cannot get Rockbox installed.
I have contacted Sandisk support, seems odd that my player will only detect 02.03.xx original firmwares.