Hi
To stop the the save file is corrupted message coming up, turn on the real time clock, close vba, and then open vba again and it should be fine - when resetting for a close frame, i think you need the real time clock off, but its been a while since I RNGd in Ruby or Sapphire
Also, in places like the Cave of Origin(Groudon's room) I had vba running at 1600%, while in Registeel's room I could only get to 1000%, so I think it varies depending on the area.
If you are going for a shiny pokemon, it might take awhile, because when I was trying to get Registeel, a lot of Method 4 spreads came up.