I've usually had no trouble with setting up a Linux NTP server in the past: currently I have one going, but some of my Windows servers dislike it. Here's some references I found to use while I figure it out...
1. Global NTP pool: use this to synch your time against.
2. A Linux HOWTO on configuring an NTP server.
3. What some of those flags mean for restricting access in NTP
4. Even better description of NTP flags
5. Microsoft's fix for getting NTP to work in Windows Server: notice the bouncing back & forth between registry, w32time, & net time.