Also having the same problem, Gotek and 3.5" 1.44MB drive installed.

Both drives works perfectly in DOS mode, only the A: drive (Gotek) shows in Windows98SE.

Was also sure I'd just hidden B: with TweakUI at some point, hiding unused drives is an old habit I've had since the W98 days. Turned out I didn't this time though. I did however notice something. In the TweakUI tab where you hide drives, B: got the network drive icon. Maybe that has something to do with it? B: is not available in the Map Network Drive dialog though.

Not that it's a big problem, can do whatever I need two drives for in DOS, but would be nice to get a solution if anyone happens to know one 😀

Edit: Found this thread. Same or at least a very similar problem. The guy seems to have found a solution, but there's no similar option in my BIOS. Maybe it's useful for someone else though.

Problem solved 😀

Booted to safe mode, where the second drive was visible and working. Iirc I installed the Gotek after Windows, might have something to do with it. Installed the Gotek as the new A drive, and the floppy was moved to B, maybe Windows didn't like that change or something. Would guess safe mode loads the floppies on the fly, not using any previously saved configuration.

Checked the device manager (still in safe mode), where two floppy controllers and three floppy drives were listed. In safe mode, device ghosts are visible too, they're not greyed out as in later Windows versions though. Uninstalled all of them, rebooted to normal mode, and let Windows reinstall them. Now both drives are visible and working in Windows 😀