I assume you are talking about Crypt::LE ? I worked on a thread with this problem recently (here).
I didn't see any documented changes to Boulder that would affect that.
There wasn't enough detail in the Crypt logs to see the responses from Boulder. If you can change the logs to provide that you might try posting on the github for Boulder. There may have been changes with, um, unexpected side effects. Those kinds of problems are a bit beyond what we could address in the community.
If you post more detailed logs we could review to ensure it looks like a bug / problem related to LE rather than your client.
That said, I agree with @rmbolger that counting on such undocumented behavior leaves you vulnerable. Even if LE discovers a recent change with the results you describe they may not consider it a breaking change worthy of a fix. I am just a volunteer here so can't speak officially.