Fleet, one of phreaky's and my games (I can't remember which) worked fine on Windows and Mac but failed on Linux because I had mixed the case of one of the filenames. If you want to support unix-based OSes, you're best off always using lower case for your files and always referring to them in lower case.
Greebo, I'm on NTFS and it's case insensitive. The only OS I'm aware of that treats filenames as case sensitive is unix (and linux, of course, is a unix OS).
It certainly won't hurt to add preceeding 0's to numbers, but if ILSWriter is using AdventureCreator, then it's unnecessary. I explicitly added the "don't need preceding zeroes" feature to AdventureCreator because when creating these games, the 0 thing frequently got in the way. I'd do one zero and not know that THIS scene went to 100, etc. When I create these games, I don't worry too much about the ease at which people can disect them with other tools. They're supposed to be playing the game, not exploring it in other editors. Especially since AdventureCreator is free.
Tlaero