I'm reaching way back in memory here, as I never did point-to-point with the GUI. (I did check the docs, though, to see if there were any disclaimers. For the batch mode, you have to use layout names rather than source, but as the CI manual does not mention this I assume it translates behind the scenes.)
Is it possible that the port you are checking is not connected directly to VDDHV? As you know, devices interrupt nets (from the net view) -- the net that goes in to a device is a different one than the one that comes out. So a point-to-point resistance report (at least as originally implemented; may have changed) shows only a nominal resistance across a device.
And just a reminder -- for final runs, be sure to leave disjoint models unconnected. (PEX Netlist Virtual Connect NO). It uses arbitrary nodes; usually safe, but who wants to rely on probability when taping out?