Sorry for the long delay! I can't reconstruct the failure anymore. Shift-H followed by Shift-G seems to work now. However, in my last game (where I reported the bug -- accidentally deleted the directory with the saved games, though) it took an insane amount of time for the scan to complete. I guess I explored too many chunks too fast.
I was playing with Cargo ships and went on a trip with the boat provided by that mod. Driving over water means you can go around biter nests, and if you stay clear of big/behemoth worms on the coast line, you can explore a much bigger area than if you're confined to land. Moreover, Cargo ships provides offshore oil (with the settings I used then, there were many, many patches) and I also used Geothermal, which spawned many resource patches as well. At one time I hit Shift-G twice and was told I'd have to wait some time before I could restart the labeling. That's all perfectly normal and dandy -- but in that case, "some time" meant something in the vicinity of 10.000 to 15.000 ticks (don't remember the exact figure). That is several minutes in real time!
Then again, I'd also YARM installed at the time -- perhaps that mod had messed with my expectations because it updates the table with values for marked ore patches automatically and I expected your mod to do the same? Seriously, I can't tell for sure anymore, but it seems I reported a not-a-bug bug. :-)