network segment gets disconnected

Sounds like an issue in the switch. What errors is it reporting in those segments when these failures happen?

i am still finding cases where one gets better connectivity if one locks fast nics media types down to the lowest common denominator, often 10mb half duplex. especially on the servers (got gigabit nics in there i bet)
here are some other ideas:
http://support.microsoft.com/default.aspx?scid=kb;en-us;325487
How to troubleshoot network connectivity problems

since you say you changed your switch and the problem is still there , you have to go down one layer lower: The physical layer . Since your connection is "partly" erratic then there is no brake in your fiber. May be your connectors or the fiber cable is damaged . Buy or borrow a fiber power meter and test the connections . Better hire a technician to measure your cable using an ODTR . That will definetly check your cabling . OR a second cheaper test : do a ping test and then an "iperf" ( iperf.exe available on the net)from a machine to another machine going through the suspected fiber link .If your link is 100Mbit and iperf shows a low bandwith like 10-60 Mbits , you got a faulty layer 1 . Next you have to check the fiber modules . If you have 2 working modules , take those 2 and replace temporarly with the suspected ones .If the fault is moved then those two modules or media converters are faulty . I don't think you have a software problem.