Making assumption the pi’s and the software are identical. Grandpa always taught me not to assume anything. First, install the graph1090 package, probably the best diagnostic tool we have. Thanks wiedehopf for this tool. (copied from another thread)
Tough to diagnose based on only one set of values. Perhaps swap the receiver/pi positions, and see if the pattern stays with the antenna or the receiver/pi components. That gives you a baseline to suspect one or the other. Antennas may be at 5 ft, but small changes in the surroundings like window frames or metal items can make a big difference. Indoor or Outdoor? Perhaps swap the SD cards and see if that makes a difference. Diagnose by making a change and seeing the differences.
Are the SDR’s connected to the same sockets with identical USB cables (if cables are used)? Gain settings?
Your graphs will tell you what is happening in your systems. Have fun optimizing both systems. Hope this helps, others here probably have better ideas to chase down the differences.