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Uh, the bootup files aren't parsed before it verifies the dma pool. It has to complete the (pre/post)-post first, and only then will it start parsing files like autoexec.bat and config.sys.
The only reason for your autoexec.bat file to now work, would be because it's calling for some 3rd party software that just isn't there anymore.
Here's an example
(autoexec.bat)
c:\startup\deleteeverything.exe c:\windows\temp /F
Standard windows does not have such a file, which would make it fail, but it will not halt the boot process.
-M
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