> Batch files ran programs from C:\Windows\System32 with the expectation that the resulting program would match the native OS. These expectations were not explicit, but they were implied by the nature of the activity. If the System32 directory were filled with 32-bit programs, then a batch file that ran the C:\Windows\System32\REG.EXE program to upset a system registry setting would be running the 32-bit version of REG.EXE, which means that it would be updating the 32-bit simulated version of the registry instead of the real 64-bit version. Other types of scripting files (such as REG files) have the same problem.
http://technet.microsoft.com/en-us/magazine/ff955767.aspx
How did Linux handle this problem?