I appears that I have misunderstood Pcbnew behavior. The bug is fixed as you said. The problem for me now was that while the all the pads on my footprint had the clearance set to 0.082 (in footprint properties), the trace/net clearances had to be corrected as well. In the picture I posted you can see that I have traces connecting GND pads and vias. These traces have different clearance defined by net-class. If I delete those traces I can route traces between the two GND pads. So in the end I can route traces between all the pads only once I have to correct the clearance in net-class editor.
Although, I do not know why I have 0.116 clearance. It seams to be a magic number. Maybe 0.2 (net-class clearance for GND net) - 0.082 (footprint clearance) = 0.118 and I just cannot measure it precisely so I get 0.116 
In any case, one mystery is solved 