There's 2 reasons I know why you get differences in pal SS's. One is that there is more than one pal region. I think there's at least PAL UK, PAL EUR and PAL AUS.
The other reason is caused by timing differences between drives in getting the response while reading the SS. These you shouldn't have to worry about, but the region code differences you do.
If the game publisher has set the region code on a game, then for example an iso with a PAL UK SS will not work on a PAL AUS 360 and vice versa.
It's also possible that there could be differences in the game itself so I guess your best option is to suck it and see...