You have hit on the exact reason I decided to abstract my controls away from using the browser detection built into .NET.  If you are using a DNN control (DNNMenu, DNNTree) in either .NET 1.x or 2.x you can tweak how the control is rendered by editing the ClientAPICaps.config file found in the js folder.  If you are using solpart a similar file SPMenuCaps.config can be found in the controls\solparmenu folder.  In .NET 1.x there was no standard for upgrading the browsercaps file, so I decided to allow the user to tweak that file how they chose and in turn tweak my file to match those. 

Browser UserAgent -> browsercaps (machine.config) -> ClientAPICaps.config/SPMenuCaps.config -> Control Rendering

For more detail on editing this file look at pages 11 and 12 of the DotNetNuke Client API doc.