I finally managed to compile GCC. I re-ran cygwin setup, reinstalled the required libs and updated some programs, and that produced a working GCC, but now I get a different error when trying to compile my kernel, namely:
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/usr/local/cross/bin/i586-elf-ld.exe: error while loading shared libraries: ?: cannot open shared object file: No such file or directory
This is the exact error that made me recompile my GCC previously. (I had simply copied it over from my 32-bit machine, hoping it would work on 64-bit also)
EDIT: Running GCC from cmd showed that it couldn't find cygwin1.dll
After adding the cygwin bin directory to my PATH the error went away.
