Couple of things to look at.
0) Can you make ANY distinction between the performance and behavior of any of the client machines?
1) Of course is my favorite – the sniffer – so that you can see what actually happens on the wire from the point where someone clicks on a link to start the intranet application.
2) Are you running a domain or workgroup? Since you mentioned clients of both XP Home (which cannot join a domain) and XP Professional (which can), and they’re dealing with a W2003 Server, it’s possible that there might be some problem with domain vs. workgroup names, or possibly some authentication issue.
3) What sort of DNS are you running (W2003?)? and if so are you allowing dynamic DNS updates?
4) Have you examined the system, security and application event logs on both the server and clients to see if there’s anything relevant?
Hope that helps! Write back with more details,