The new test case that constantly causes reconfigure has uncovered a bug in the way the checkpoint server thread works. If it is reconfigured in some combination of enabling and disabling log and time based checkpoints it is possible that the server will miss a signal on a condition variable and end up waiting forever.

The particular condition wait in question is:
https://github.com/wiredtiger/wiredtiger/blame/master/src/conn/conn_ckpt.c#L98