When you line hone (or line bore it) you (usually)cut the caps, making the hole smaller and out of round. Then you hone or bore it back to round. Everything is now back to size. Except for the seal channel. It was made smaller, but the process to get everything back to size doesn’t make the seal channel back to size and it’s now smaller.
Now the seal has way too much crush on it, because the ends of the seal are too proud, not only on the cap but on the block. When you crush it that hard, it goes out of round.
The only way I know of to fix it is to shorten the ends of the seal until the seal is not getting its brains crushed out. I do it with a belt sander and just lightly sand down the ends as equally on both sides as I can until the crush is correct.