Good to know!
Regarding the floppy drive, using Disk Management in Windows (help given in my link above, at least for the latest OS, for XP the link is dead...) to change the drive letter may be easier than using the BIOS, if possible.
To go back a bit on what I wrote on virtual drives, latest Daemon Tools or Virtual Clone Drive should discard your virtual drive when the CD image is unmounted, and they don't automount to A: or B: by default. So at least this makes things easier - no need to check your drives if you're not mounting something.
I've had other issues with A: drives lately, sometimes with mods, others with installers. It's like D: partitions and some EA games like Alice Madness Returns, which refuses to install there. For example, CubanRaul's patch for Blood Omen (which is essential to play the game on current systems) has an option to install the game directly. However, if your CD image is mounted on A: (and maybe any drive letter before your physical drive's), the installer won't find the CD. And so on. It's like they prevented people to use floppies by mistake, or from installing on system drives like D: (well, I remember D: was a popular letter for Recovery partitions). I don't know why Sea Dogs does that, but yeah: A: drive is cursed.