This issue has been around for a long time (potentially UE3).
UNetDriver::Time is a float, which is updated by accumulating Delta Time during ticks. This means the longer a game runs, and the higher the server tick rate is, the more likely it is that floating point error can cause the time to never properly update.
This may cause a number of issues, but the most apparent seems to be that Handshaking fails so new clients can no longer connect.
The client connects with no issue.
The client connection fails, appearing as though the challenge fails.
This is only one instance of the issue, but there are potentially numerous other side effects.
**Note: As of 3825875, the above repro was worked around. The underlying issue still persists.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-53832 in the post.