9 times out of 10 it is a problem with the non-Cisco equipment. However, all those potential problems need to be discovered ahead of time (during design/discovery phase of project). In my experience other gear either does not do QoS or does not do it well, has fucked up POE or a myriad of other problems. You get what you pay for, in short. A lot of other gear is OKAY at simple switching/routing but anything beyond that is iffy.
Now, some the proprietary shit that Cisco IPT gear can do with Cisco switching gear is a PITA to work around if you don't have Cisco switching gear. However, it CAN be setup that way and it would be no different that another decent phone system.
I can't argue much for the Nortel/Mitel side. I've worked for a Nortel Partner that focused 90% there and 10% Cisco and Nortel is downright pathetic. I've worked with Mitel partners and if it is small business it would be OK in comparison to Nortel.
My '03 Sold.