I might can answer some of the questions, but i cant say for sure, thats this is the problem or thats the problem.
If you have a router between your server and internet and you only forward those ports that are need, i think it was from 29070 to 29081, be happy about that, thats just good for your server and the protection of your server.
If you have 1 netcard on your server, make sure, its working, sometimes netcards can have invisible errors, you ping and stuff, looks like its working, but its not working.
Also your bandwidth is importen, the more the better.
If you have 10 mb bandwidth, dont use a 10 mbit netcard, use higher then 10, 100 mb is recommened.
If you have 2 netcards, dont use any cheap netcards, use alittle bit more expensive and install those netcards right after the AGP Graphic Card so its
AGP = Graphic Card
PCI = Netcard
PCI = Netcard
Remove or disabled sound card, If you also are playing from the server, then leave sound card or enable it.
Talk to your Internet Service Provider too, they can have couple of switches that causes the disconnection sometimes and sometimes there are no problem.
You must also play on other servers to see if you get connection interruption or not, to make sure that it might not be the ISP´s side, it could as well be on the other server ISP Side.
If you use wireless network from your internet connection to your server, that should be a bad thing says people, I personally dont know, never had Wireless, but those who complains on my server, are those who has wireless. ( Dont know if i should beleave them or not, i still prefer cable network :P )
On the Jedi Server side, there is alittle bit configuration to make too.
I have sv_maxrate "25000"
and clientside /rate 25000
server side = sv_maxrate "50000"
clientside = /rate 50000
More then 50000 = no effect at all dont even try it.
Make sure your Windows or linux is patched, dont install too high required virus scanners or firewalls.
Simple one for Windows XP or 2000 Professionel you find it on this one www.free-av.com
( its free and a good Virus scanner ).
Make sure that you also are protected against this = jamsgbof.cfg. You will find it on this link
Little bit more server side stability.
Dont use more then 16 players on the server side, the server can crash
when i switched to sv_maxclients "32" server crashed after 15 to 30 minutes, it also crashed after map switch, it happen 2-4 times, now max clients are 16 and it stays there.
Try also to add your server.cfg file, i might can identify something that i can recommend.
You have the same problem as i had in 2004.