By strict definition, you're not really 'keeping it in the box.' You're sending a Nuendo track through the DM in order to obtain a DM 'verb effect. In the box means just that - the DM is merely a control/monitor surface, and all audio, efx, plugins, fader levels, and ultimately - the summed mix - is performed in the computer.
Again, use the OUTPUT SLOT tab - NOT the Output Tab - to route dry signal directly from your preamp(s), to DM's ADCs, and into Nuendo. This way, you can still monitor your input sources without stepping on the signal by adjusting anything in the DM's channel modules.
I can't say for sure what's causing the 'verb hanging; could be many things. If you have time, I'd suggest uploading your DM screenshots here - specifically the Input, Output, and Output Slots page. As you know, this can be done with TMC.
CaptDan