I've been struggling with something similar myself and since I started kegging some batches, I notice that the flavor is definitely not present (or much less so) in my kegged beers. This was an issue both for my first few extract batches and the AG batches that followed.
I can't put my finger on the flavor exactly, but it's sort of stale.
I don't know enough to say what it is, but my best guess is some sort of oxidation from the bottling process. Two things lead me in that direction: I notice this most on hoppier beers, and I also notice some variation from bottle to bottle. It seems like the ones that have a high amount of the this off flavor have almost nonexistent hop aroma/flavor. In the bottles that taste better, some more hop aroma seems intact.
I know the inconsistency could point to sanitation, but I'm pretty meticulous about cleaning and rinsing bottles well, sanitizing them, and pulling them straight out of the starsan before filling. In 15+ batches I have never had any bacterial issues. Additionally, I do not notice this flavor at all when kegging.
I think my next troubleshooting step may have to be something along the lines of separating the bottles that fill quietly from the ones that have a bit of splashing right at the beginning. This would allow me to compare those bottles and see if that makes a difference. Next step would be trying a batch where I purge half of the bottles with co2 before filling and compare those to the bottles that haven't been purged.
Best of luck figuring yours out, hopefully someone here may have some insight as to what is going on.