Unfortunately I no longer have my old GCC3 toolchain I used with cygwin, so I can't produce executables that are stable. I once tried to build it from source by applying patches, but had no luck. GCC becomes increasingly difficult to compile as the version number difference gets bigger.
When multiple things change it can be difficult to say what broke something. Often the only solution is to revert things one by one until you find the culprit.
I have no problems with saving, directory creation and the rest works fine here.
It should be set to no, it's no longer publicly available for the time being. The 1.5.10 version you linked doesn't work for me. It produces a lot of illegal memory accesses and it has broken in-game grahpics.
I never had this issue, but compiling the game with the new toolchain is probably not a good idea. There are some optimizer issues causing random crashes I never managed to track down.
r_bsp.c: fixed an unused variable warning
commented out some dead code (software poly renderer, R_Gen*Tile, R_EntityParticles)
early return for SCR_DrawFPS