floppy drive works only in windows

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I'm having trouble booting from/accessing my floppy drive (general failure reading drive a:) but it works just fine in windows 98se. what could be the problem? everything seems fine in the CMOS setup, the cable and drive seems fine because it works in windows.
 
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The light is okay. Yes it happened only outside windows when you go to ms-dos command prompt. But it can access the a: through the window 98se's ms-dos command prompt( start menu > programs > ms-dos prompt )
 
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you're not doing anything weird like using one of those PCI cards with a built in floppy controller, as your A drive controller are you?

I've seen those for sale, and have always wondered what kind of mischief they might cause. I've not had the opportunity to test one though.