My guess is that your primary controller isn't releasing the IRQ and DMA
lines when bit 2 in port 3f2 is cleared. Not all controllers do.
If this happened to our customers, we usually told them to use a different
DMA and IRQ for the second card and adjust their DISKETTE.CFG file
accordingly.
We used to offer a diskette copyring program (SyDupe) that could use up to
three controllers all on different IRQ and DMA to achieve three completely
overlapped data transfer paths (i.e. we'd write three diskettes at the same
time). This worked for 720K, but 1.44MB put too much of a strain on most
ISA bus implementations to be a reliable product. Still, it was kind of
neat to see the product working with a loaded (12 floppy drive) system.
Cheers,
Chuck