Well, I never really experienced this problema. Let me tell you how I do it.
First of all, I take USB, plug it into the PS3 USB port, then go into the PS3 SaveFiles, then see which game sabe I can actually copy onto my USB. For example, Megaman 9. I copied it onto the USB, unplugged it, and plugged it into the computer. You will have 3 files within each other. PS3 -> SAVEDATA -> (Insert name here). You want to delete the file with the save you copied from your PS3, the one at the very end. After that, just drag your newly downloaded sabe, courtesy of "domthybomb."
Or if you wanna be quick about it, just plug in your USB, make a file with the name "PS3", then another saying "SAVEDATA" and then after you go into the SAVEDATA, just pop in your new save. Plug it into the PS3, go to the save files, go to usb, press Triangle, Copy and voila! You should be done and it should be working perfectly.
Hopefully this helps even though its a long ass message.