I realize this thread is 6 years old, but it come up in google when searching for this issue.
I have for years struggled with bad off flavors as described in the OP. I have recently begun to focus on this issue, and recording when I use a paint strainer bag and not. I believe I do get a bad flavor from them. (I often use one in the boil).
The off flavors seem more common and stringer now. One theory I have is that I used to reuse the bag quite a few times. In the past year or so I've gotten lazy and tend to throw it out after one use, so the bag is always new. I believe the off flavor diminishes after a couple boils.
I strongly recommend NOT using the bag and taking note to see if your off flavor goes away. What I do now is just throw the hops right in the kettle, and post boil and chill, I tilt the kettle back (raise the front up an inch) and give it a half hour for the hops and break to settle in the back. The I tilt it forward again and rack to the FV, leaving behind as much wort as I need to keep the sludge out. If you have to, brew 1/2 gallon more than you want and leave it behind. It's worth it, and not very expensive (the cost of a paint strainer?).