Recently had a new standing seam metal roof installed. Roofers could talk the talk but I was not impressed with the quality of work overall. My main complaint is that they installed the roof so that most of the sewer vents go right through the middle of a seam. The boots are clearly not designed to accommodate this and they've succeeded in creating more work for me in the future; which is what I was trying to to avoid by spending the extra money to upgrade to metal. The boots are going to leak. In fact, they already have.
I was pretty pissed about this initially and told the owner of the roofing company that if they had bothered to tell me this was going to happen, I would have moved the damned vent pipes myself if they weren't going to. The right fix would be to replace the panels and move the vent pipes but I have a feeling getting them to do that is going to be difficult if not impossible.
Is there a boot that's designed for this kind of install or a better way of sealing these? Or, am I going to be stuck checking and resealing them every couple of years?
Not sure why no one sees this, so maybe I'm wrong, but the seam on standing seam is not sealed, just snapped together, so water will simply flow into/under the top of this boot no matter how well sealed it is. OP started it's already leaking, and of course it is, there is no way to seal this properly. I put the same boots on my roof and made sure they didn't span a seam, works great. OP your roofer doesn't understand the fundamentals of standing seam. You are correct you probably need to replace both whole panels and relocate the vent or get a metal roof specific vent flashing.