I am glad it worked out for you. That sure was a strange problem when you figure the 6.5K middle pickup up on Texas Specials is the reverse wound/polarity pickup and the neck and bridge are the same polarity
This is how Texas Specials are according to Fender specs.
Bridge 6.5K 7.1K -- 3.58 HEN.
Neck 6.2K -- 2.4 HEN.
Mid. 6.5K -- 2.6 HEN. Reverse wound Hum Canceling

I seen it though most times its because someone put pickup in the wrong way. Or they don't have what they think because its hard to buy one pickup from sets like Texas Specials that are new and not scavenge.

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The strongest reason for the people to retain the right to keep and bear arms is, as a last resort, to protect themselves against tyranny in government.

Thomas Jefferson

Exactly, Idid have to swap the wires on the bridge pickup to get it to work though.Initally when i first installed the bridge pickup a few years back,the bridge was out of phase with the middle, so I swapped the wires.So when i changed the neck and middle today my thinking is that the bridge would go back to normal, but it didnt.So the black and the white wires are reversed still, but everything is working the way its supposed to.It has me thinking that I wonder if the Texas Special Fat Strat pickup polarity is reversed to accomodate the seymore duncan pearly gates.Just a thought.