Yes, this sounds strange. Let me explain. I see this with two of my configs, one that Yang.Y spent considerable time helping me with about a month ago and another that is a fairly typical tunnel to multiple hosts. I can provide exports if needed.
Basically all SSH passwords that I will be discussing here are one-time passwords. Once they have been used they are invalidated. This is important to note as you will see shortly.
Basically, on any given work day I go about my business and Core Tunnel happily does its job without calling attention to itself. Thanks for making such a great product! At the end of the day I shut my MacBook and go home. The next day, I open up my MacBook to begin work. After a moment Core Tunnel figures out that two of my tunnels are down and attempts to reconnect. It displays the first of two password prompts. So far this is all entirely reasonable and as expected.
The problem arises when I enter my new password. Core Tunnel essentially ignores it. I can tell because the dialog disappears, then another password dialog appears(second tunnel), then disappears when I enter my password. At this point the main screen of Core Tunnel shows trhe two tunnels disconnected. If I then click on "Connect" on one of these, I am prompted for my password and this time it connects. I know that the password was not used on the prior two attempts or it would be invalid at this stage.
If there is more I can do to help characterize this problem I am happy to.