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Precision pickup orientation?

Weird and probably stupid question, but here goes.

Does the orientation of the pickup matter? More specifically, I've flipped the top pickup so E is now A and vice versa. After I shielded the cavities of my P bass, I noticed that if I flipped the upper half of the pickup, I would have more wire to work with making my life easier.

The only reason I'm asking is that the A string now sounds like a slight reverse envelope filter is being applied when a sustained note rings out. It's only happening on the A string. I don't know if this matters, but it's a Duncan SPB-3 and the strings are medium chromes.

To be completely honest, I don't know if this was happening before I flipped it or not as I only played it briefly before I got around to shielding it.