I read a while back that there are certain commands eg copy that under Win7 64 bit are actually 32 bit applications, not 64. Can anyone elaborate? If Im right, this means that they will need WOW64 to run correctly. The reason Im asking is that we have a few scripts that, when run manually, run fine but when run through Scheduler, sometime run fine and sometimes cause cmd.exe to crash. I was told that WOW64 is unstable and this is what causes the issue.
What you describe in your comment gives me the willies! That sounds like bad RAM, a bad I/O controller, etc. That's definitely not normal Windows behavior.
The Windows on Windows 64-bit environment (WOW64) is pretty mature. It has been around since Windows Server 2003 x64 Edition and I am not aware of any reputation for "flakiness". I think 64-bit Windows gets a bad rap mainly from devices that have only 32-bit kernel mode drivers available, and from its inability to execute 16-bit applications. Neither of those things, though, are anything like what you're describing.
I think you might want to consider starting the migrate to PowerShell, for this and a whole bunch of other good reasons. There's a very good set of lessons here.
(I would comment above, but don't have the points for it yet. But I will say this, I just checked and think I first used cmd over 30 years ago. It's had a good run.)