OK. So a few years ago, I decided that using floppies with my game doctor SF7 was just too much of a pain, most of them didn't even work.
So, the solution? Replace the floppy drive with a USB floppy emulator! On the one I got, it required a 256MB USB stick and had 100 virtual drives, which I'm still unsure how it does, you can plug the USB into a normal PC and it'll pick up the first floppy and show you a 1.44MB drive, you can format it to the full capacity, and the person selling them gave me a program so that you can switch through all 100 virtual drives on it, nifty!

Anyway, one real annoyance of this is the way that the game doctor reads the floppies; the disk drive is in constant use, checking if a disk has been inserted. This is fine for 512KB or 1MB games, but anything over that's been split and is on more than 1 virtual disk will fail, well at least with my drive they do. So I needed a solution that allowed me to change the virtual disk number whilst the game doctor was checking the drive and after a bit of fiddling, I managed to find it!

http://cgi.ebay.co.uk/3-5-1-44MB-USB...item439f49bb63

That's the one I have.
So if you want to do this fix, make sure you've got some experiance with soldering, and that you've got a small switch (I used a PCB switch that I salvaged off some old board) and 2 wires.l

(Sorry, I didn't take pictures of this so you'll have to just follow along).
Open the drive up and remove the top cover (4 screws on the top). Then unscrew the PCB (2 screws, one next to the USB port and the other next to the floppy interface). You should see a jumper too, installed onto the marked J1 and S1 pins, remove it.

Take the PCB out and flip it over, solder the wires to the two points of the jumper you just removed (J1 and S1). Solder the other ends of these to a switch (PCB switches with 3 legs; solder one to the middle and an end one, and the other cable to just the other end one). Now that's done: Test it to make sure it works. Then once tested working, you need to make a place on the front cover to put the switch. On mine, I had a grooved bit of plastic above the buttons (my LED is square, on the right, older model I guess) which I drilled out, and hot-glue gunned the switch into it. I also had to slice a chunk out the top cover to give room for it to fit back on. If your fix doesn't looks anywhere near as terrible as mine does, chances are you probably won't have to.

Reverse back through the instructions (place PCB in, screw both screws in, do NOT put the jumper back in, close cover, insert 4 screws and install back into game doctor).

Now the way this works is when loading a game or being used generally, the switch is left connected, but when the 'insert new disk' appears when loading a multi-disk game, flip the switch and you can now change the virtual disk number, change to the next disk and flip it back and the game docter detects it and loads the next file!

Hope it helps anyone with a similar problem! :)