I recently purchased a Dunlop Jimi Hendrix (JH-1) wah.
This is the first time I have ever used a wah pedal.

I have a standard Strat and use a solid state Fender combo.
I also use a Zoom multi pedal or a good ole' Boss DH-1

When I am playing with some gain and I have my heel down, when some of the lower notes ring (especially F# and its power chord) it sounds like controlled feedback. (some of the middle range notes don't make this feedback, only near the nut on the E string)
I mix things up with gain settings, pickup selection, etc. and I still get this "feedback-y" sound.

Granted, you can still sort of identify the note, but with the heel down, is it supposed to have a feedback sound like that?

Any answers or suggestions would be great
The wha sweeps through the tone ...

heel down = low end (thus more "feedbacky" sound

toe down = high end (brighter, thinner, more sustain)

so yes, it is SUPPOSED to sound like that

Best sound for chords is somewhere just past the middle - you'll have to play with it until you get what sounds best for you.