Have you checked if the second floppy drive is connected correctly on the cable? Should be 2x connectors for the 3,5'' and 2x for the 5,25'' - kind of like two "channels" with two connectors, and you can only have one drive per "channel".
Also, check the BIOS settings. I'm not sure if the BIOS/motherboard manufacturers take into account the possibility of anyone still using a 5,25'' drive anymore. Ditto about operating system developers.
You might want to try to hook that drive up to an old PC - something like a 486 or Pentium 1 - running a similarily old operating system - DOS, Windows 3.1, 95 are the best bet, perhaps 98 too.
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