Unfortunately, it's a natural phenomena with those vehicles, even when used responsibly. The smaller tires and increased slippage naturally erodes the finer particles in the road surface from the larger rocks. Then, once the larger rocks are tuned loose, their narrower "gauge" effectively narrows all the roadways through their rock-churning action. Heavy, long-term use on dirt roads is nearly incompatible with typical over-the-road vehicles...and unless you blade out all the rocks and effectively lower the road surface to "new" dirt you'll never make an effective repair.
This is very apparent on the road above Eureka, particularly near the location of the original SN snowshed. There is also a portion of the SRR grade below the Genessee Vanderbilt dumps that has been pretty worn out - and that was occasionally a goopy area to begin with.
If you want to see some "pristine" grade that isn't driven on, I highly recommend the hike out to the SRR turntable and then down to Ironton. The short hike around The Knob from US550 to Red Mountain townsite is also fun.