Any suggestions?

The only thing I can think of is that theres perhaps a jumper on the drive OR you could try using a cable with a different "twist" in the cable

K, thanks for the input, I'll try that.

Okay, I found out what model number it is, it's an EPSON SD-800 Epson SD-800 combo drive I already found one post on here about this kind of drive, I will do more googling to see what I find.

Okay, I found out what happened, might make this one reply a stick or something. K, here is what was going on using the info in Malik's post

I'm using one of these drives in my 486. […]
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I'm using one of these drives in my 486.

To use this :

1. You need a 5.25" floppy connector to connect this drive to the motherboard.

2. In BIOS, in the basic setting (eg. the first option in Award Bios - where you set the type of hard drives and date and time), set Floppy A to 1.2MB and Floppy B to 1.44MB.

3. You can set the "Seek Floppy Drive on Boot" in BIOS to see if they are connected properly and to see which reads first (- A drive).

4. You can now use the BIOS option "Swap Floppy Drive" if you would like to choose the 3.5" slot as the first, A drive, which automatically changes the 5.25" slot(drive) to B.

so, since the picture says that the top connector (the one with the twist) is slot/drive A I swapped to the top connector, booted into windows and it was still swapped, but this time I saw that the 3.5" was in the Z position in windows explorer but then you clicked on it it still tried to read from the b drive (5.25"), I remembered that in all my trouble shooting I swapped the drives i bios (slot A was assigned to the 5.25" and B was assigned to the 3.5") so once I changed that in bios windows shows them in the proper order, the proper one reads from the proper drive and it even boots off of the floppies properly now, so I didn't have to mess with jumpers, it was just a simple cable bios conflict.