Alright, I can fix this for you. I had the same problem and figured it out on my own, then emailed ryleh and asked him specifically.
Note, this is VERY easy to do through windups.
Edit: You can do this with either the .ST0,.ST1 ect files or the SRM files. .ST0 ect is the save state, SRM is the SAVE file itself.
What you do is make a NEW folder and move the SAV files to that directory. COPY PASTE. DO NOT DELETE THEM. Once you have confirmed they are both in the NEW folder and in the SAV folder, then you delete ALL the saves from the SAV folder.
Now all your saves are in the NEW folder.
Now, go into Pokemon or whatever game in question and save a state. It will create that state in the SAV folder. That ID number on the newly created state is the ID number for that game. WRITE IT DOWN.
Now delete the new save from the SAV folder.
Next, take ONE save out of the NEW folder and COPY it back to the SAV folder. Now you have one copy in NEW and one copy in SAV. Rename the save state in the SAV folder to the new ID number that you wrote down.
Load that state.
If it does not work, delete it out of the SAV folder and move to the next save state.
Repeat. (COPY, RENAME, LOAD) until it loads your state. Do it for each game you need to restore the states to. I highly suggest that you complete each game one at time before you add more roms. I know it's tedious but he told me the next release will fix this. Probably name each save with the name of the rom, so that you can make this much easier.
However if you are going to add more roms, and want to avoid this, then you have to make sure that you find out what state goes to what game, and MOVE each state and RENAME it for backup purposes, then do this process after you have added more roms.
Don't worry, don't panic. I just hope that nobody has dumped saves because of this. I hope this helps.
~Steve