Question : Intermittent Lost Network Connections

I have a LAN that comprises of 42 x 3com 3824/4228g/4226 switches.  The top level switch is a 3com 3824 gigabit switch which connects other buildings over fibre to 3Com 4228g switches which in turn drop down to 4226 switches.  All WAN kit is based upon Cisco technologies i.e. 3600 routers, Cisco PIX's etc. to interconnect ten UK offices back to HQ.  I use What's Up Gold to monitor the entire network.  The problem encountered is only apparent at our HQ site.

Periodically I receive reports of loss of network connectivity i.e. lost network drives (Netware 6.5) and What's Up Gold reports the loss of a few switches.  There is never a pattern to which switches are lost.  What's Up Gold is set to poll every 20 seconds and notify me in the event of any packet loss, sometimes I get text alerts from WUG informing me that switches have missed a poll.

All switch to switch connecting ports are set-up to be auto with only the 1000/FD or 100/FD advertised depending on what they're connecting to i.e. gigabit to gigabit set to 1000/FD and gigabit to 100m/bit links set to 100/FD.  Flow control is set to on (I believe this only makes a difference at FD), as is broadcast storm control and rapid spanning tree (although I've noticed a few switches are actually set to 'spanning tree' rather than 'rapid spanning tree'.

I've tried using the 3Com network Supervisor/Director software to check out mis-configurations, however the software does not find all my switches when searching a subnet, those that it finds are not always in the correct topology.  Had some very strange results!

I've checked the ports of workstations that most common report issues and found that they have a higher than normal (set to 100/HD) collision count.  These workstations are generally CAD stations and therefore the size of files being saved are >25mb.  Investigating the workstations I've found that some are set to auto negotiation whilst some are hard set to 100HD.  On the switch to workstation side, these ports are set to autonagotiate 10HD/100HD since he have a mixture of PC's running with 1000/100/10 m/bit cards.

My queries are (sorry for the amount of them) :-

1. Is packet loss using tools such as WUG or ping normal for a switch i.e. does the switch prioritise traffic when under load?  

2. Which version of spanning tree is recommended i.e. 'spanning tree / rapid spanning tree' ?

3. Why would the 3Com software give such strange results?

4. What is the recommended switchport to workstation settings?

5. I realise that collisions on a HD connection are normal but at what percentage ?

Any idea's (500 points!!) ?

Answer : Intermittent Lost Network Connections

1: yes, packets are always confined to their respective queue, but it have no effect since the queue are empty most of time.
2: Link resolution is much faster (less than few seconds) with RSTP than using STP that normally take 30 seconds to respond.  Also, mixing both protocol isn't a good practice and may cause problem.
3: hmmm  Do you have VLAN that are not trunked over all switch fabric?
4: default autospeed-noflow.
5: 5% is normal, 10% acceptable, over that i would consider another solution.