I was suprised that the no flap t/o run was the same.
The take-off run to rotation is a simple linear acceleration and there are only two factors important: Thrust produced by the engine, and aircraft mass. Both are not influenced at all by the flap setting.
Theoretically speaking deploying the flaps adds drag, but since the wing is hardly producing lift (as the AoA is close to zero), the induced drag from the flaps is virtually zero too.
Not entirely zero though, and that tiny little bit is the reason that people like Morrisman1 do the initial run at zero flaps, only selecting t/o flaps at the last moment. But that's just to squeeze that very last bit of performance out of the aircraft in tight situations. In your situation, I don't think you'd have the proper instruments/measurement tools to actually notice the difference. And this technique is not mentioned in the PA28 POH, so Mr. Piper apparently also doesn't think it makes a significant difference.
The reason for setting t/o flaps is that you can rotate at a slightly lower speed (but what's two-three knots between friends?), and get the best (angle of) climb performance straight after rotating. Setting flaps also increases the average angle of incidence across the wing, which in turn reduces the required fuselage AoA and allows you to see straight ahead over the nose better. And in certain aircraft you need t/o flaps to avoid a tailstrike upon rotation.
Where did you get the 52 and 55 numbers from by the way? I have a PA28-161 Cadet POH here and it specifies a rotation speed between 40 and 50 knots, depending on actual weight, both for normal and short-field t/o. Now the Cadet has a lower MTOW than a normal spec Warrior, so your -28 might have a graph extending all the way up to 55 knots or so. But you were not nearly flying at MTOW, so my gut feeling tells me that your rotation speed should have been around the 45-48 knots mark or so. Did you look at the POH for correct technique in both cases, including proper speeds? It takes book technique to achieve book performance, after all.
And speaking of the POH, I just checked mine (as said, for the PA28-161 Cadet) and the t/o roll for 0 and 25 degrees flaps in similar conditions is virtually the same. If there's a situation where the difference is more than 100 feet, I didn't find it.