I have the same problem on my copy of Windows 7. I think Windows doesn't like people using the root of C drive. Making a directory in C drive called "ROMS"(or whatever you choose), and in put your 3DS roms and rom_tool in there. You should be able to use rom_tool in there without problems. And I'll see what I can do about making a MAC compatible version of rom_tool.Thanks for quick reply!!!
Rom is on c:\
Romtool is in same root dir
Os is windows 7 32 bit on mac. (Tried using fusion and a complete reboot into native windows using boot camp)
It may be a mac / pc compatibilty problem but running windows natively using boot camp (should) be exactly the same as running on any window pc.