Comment by jeroenhd
Let's Encrypt doesn't work great when the Let's Encrypt client software has a bug or is misconfigured (one of those is true for your situation).
I think keeping the validity long just removes incentives for people to bother fixing their setups. We've seen the shift from "Craig needs to spend a few days on certificate renewal every year" to full automation in most environments when the 90 day validity period was introduced, and shortening it to a week will only help further automation.
You'll always have the option to skip the hassle (for a small fee, unless a Let's Encrypt competitor joins the market), but I feel the benefits outweigh the downsides.
I personally would've preferred something like DANE working, but because the best we've got is DNSSEC and most of the internet doesn't even bother implementing that, I doubt we'll ever see that replace the current CA system.
I cannot say that this works as flawless as some would advertise, with just as script running every 90 days. Some services do not load certificates while running and must be restarted. That alone can be a hassle.
Some software now uses short lived certificates and even with decent configurations, there is an elevated level of problems specifically because of certificates. Especially in networks that use a lot of segmentation with very restricted network traffic.
I think a short lifetime can be a security benefit, but it should not become a dogma. It should be employed where it really makes sense but as a general rule inconvenient describes it quite well.