This is a huge issue with running windows servers. When we publish for a client, we always check the "Generate Short ASCII file names" in the publish options. We have run into many problems if we don't do that, because the file names are too long for the server.
Note for controlling file names for external html objects that use the file names as a reference (like a menu), keep the chapter and page names short and it will help this situation.
We deal with this all the time, let me know if you have any specific questions: gmoore@i3logic.net
Thanks!
Greg