Personally...
If it is only 2 of 60 users I would be looking more at software on their PCs.
Again, especially firewall and AV software that can intervene in the POP collection process.
Just an example, but if they both had Norton 2003, Norton maybe released an update to the mail proxy, both PCs exhibit the same timeout problem...
I would get them both to temporarily disable or remove any AV or Firewall. (Ideally from inside your network so they had some protection

)
Spyware is also out of control recently. I had a guy come in with mail problems, but removing a tonne of spyware (using adaware, spybot, cwshredder and Hijack this), updating his AV and running Windows updates, solved the problem....