Hi Nikolay,
This is not a bug. The MakefileGenerator script is quite platform-dependent, so the executed code varies from Windows to Linux/FreeBSD or Mac OS X. Hence, the checksum is not the same in each case. Simply clear the MD5 checksum on the Script tool, and it will allow you to execute the icon without problems.
On a side note, why do you need to run MakefileGenerator on different platforms? The generated makefiles and project files will be the same, so in principle you only need to execute it once.