Change the "Pour over same net polygons only" setting to "Pour over all same net objects" under that polygon's settings. (See your second image.)
Also, the polygon clearance from GND shown in the first image looks weird since it appears to only be creating clearances from the trace and not the pads. The other net clearances look reasonable, so the problem may just be a result of your various attempts to fix your original problem. If so, you will want to revert some of the changes you made to the clearance rules as you were attempting to troubleshoot your polygon problem.