Yes it is a common problem, Brian has addressed it stating more or less that everything would be have to be rewritten, something about it leaking memory like mad. since these problems primarily occur with win98 and aren't quite so frequent with XP I would strongly suggest trying to use that.
I don't know if the new SCIstudio will have this same bug, I don't think anyone has ever said but since it is an extension of the current studio I would probably say yes.
If you can find it Nychold has reworked scistudio somewhat to suuposedly fix this, I haven't tried it so I don't really know. Somewhere around here, one of these threads, Nychold mentions it and I think there's a link but I don't know where the thread is right now so I'll let you search for it.

p.s. with xp often times when getting that error you mentioned, you still have an opportunity to save your game. As you will notice when you click on ok nothing happens until you click something else, make that something else the save button and that crash ain't quite so bad.
p.s.s the cascading error, the one that doesn't stop, it sucks.