The problem is definitely within your system.
As unusual as it may seem, to me there can only be a few places where things could go this way:
-
IIS
[has anything changed recently] -
certificate store
[has anyone added/removed any certs recently]
I'd review recently applied Windows Updates for anything cert related.
I'd also try issuing a cert from another CA to see if the LE is actually part of this problem [or not].