You should open a support case so they can assist with troubleshooting. We have a tool that can be run from UDT against network devices to see if they support the MIBs we need. If you run that against the 2960/50, it should tell you if that is where the problem is. Are you running relatively recent IOS code on those devices? The switch itself might not be populating those SNMP values.
The reason they are showing up on other switches is probably due to the fact that MAC address or ARP table includes information about those devices. This could be due to layer 2 domains spanning the network. The devices should show up as indirect connection (meaning the switch knows about them but they aren't physically connected).
I have the same problem the gentleman who starte this thread. We're a very big NPM shop for over 5 years and we're running an eval version of UDT as a stand alone set up as to not mess up our NPM install. The problem actually extends to Cisco 6500 devices too, which is Cisco big enterprise product. I haven't checked it on Nexus device yet.
So having said all this, I remember the same issue existed on Engineers Tool Set V10.0 Switch Port Mapper. I have a copy of that version as well as a newer copy of Ver10.7. Sure enough, the problem does exist on Ver10.0 identical to UDT V2.0 and it doesn't exist on SPM Ver10.7. On the surface, it would appear that your developers have built UDT on top of the older code or built in the same bug. However, it could be this is a new bug. Having said all that this is a serious enough issue that your developers need to jump on this.
I've been working with James Cutrer in Sales, so he has all this information and I presume he's going to have a Sales Engineer look at it. I'm open to a webex to show the issue and all my tests
Also let me add, that I wrote a report against one of the routers that was having the problem, The report is written to show connected MACS and IP addresses, The DNS name of the connected device shows up correctly next to the device port but th # of connected MACS and connected IP's shows 0. Some of the info is being collected