hey all, the high e string on my nice new guitar seems to be going to shit and I'm worried the b string is on the same path

the high e string had an almost totally dead tone on most of the frets but through adjusting the string height and waiting a week or so; the dead spot is only a few of the higher frets but still an obvious dead spot, the b string does not sound right either like it's too twangy or muffled or something which is how the problem on the e string seemed to start

what seems curious is the bridge pin for the high e string is almost twice as far in as the other five pins; you can very obviously see that (which confuses me because you would think the guitar would come with the pins as far as they could go), the b string is about 25% farther in than the four lower strings that are all uniform

this seems to correlate well to the problem but that was the first thing I pointed out to my guitar teacher and he said no no no, that's not it, can anyone help me out here?
Just be careful you don't crack the bridge trying to force the bridge pin in all the way. I think that's what caused the crack in mine and it was also the high e string. Roll up some some sandpaper in a cylindrical shape and sand out the hole(little by little) until the pin goes in cleanly but snugly. On my guitar this didn't affect the tone in any way or cause dead frets, still played and sounded well. It could be uneven frets or maybe it needs a truss rod adjustment. I'd start with sanding out the hole and getting the pins in though and go from there.
I would expect the tightness of the pins to have the slightest effect on tone, provided that the string balls are seated properly against the bridge plate. Sometimes a tight pin causes the string end to jam in the hole without being properly seated, but this usually causes the pin to lift out when the string is tightened. However, I see tight pins as a liability, and ream out the pin holes on all my guitars so that the pins are a drop fit. - Sometimes they are only held in by the tension on the string ball.
As Tony says... As long as the string breaks properly over the saddle, the bridge pin should have little or no effect. Dead spots are more likely to be a problem with the frets... A high one somewhere causing all the notes "short" of that one to sound the same.