Salectric, my guess is that the different grounding wires probably made a difference in the amount and/or frequency characteristics of ultrasonic or RF energy entering the phono stage. Either by making a difference in the effectiveness of the shielding provided by the enclosure, or by differences in antenna effects.
With many and perhaps most phono stages audible differences can be expected to result from significant differences in ultrasonic or RF energy that may be sent into them, as a consequence of intermodulation, demodulation, and similar effects. One evidence of that is the number of threads we've seen here over the years in which people have reported problems hearing radio stations when listening to phono sources.
Were all of the wires you tried approximately the same length, and were they routed and positioned similarly, relative to other cables, power cords, and components (especially those containing digital circuitry) that may have been nearby?
Length differences would affect inductance, which would affect grounding effectiveness at ultrasonic and RF frequencies. Significant length differences might also result in differing antenna effects. Differences in positioning might affect pickup of ultrasonic or RF energy radiating from nearby power cords, cables, or components.
Regards,
-- Al