Could you explain what you mean by sent beyond the scheduled time? Do you mean messages for which Thunderbird was offline when the message was scheduled to send, but it was picked up correctly next time Thunderbird was opened, and not deleted from Drafts? I'll look into that. I suspect it has something to do with interacting with IMAP folders immediately after starting Thunderbird.
The column has been having all kinds of problems with sorting, persisting in the same location if you drag it around, and when messages are scheduled/rescheduled. I know this is annoying, but it's something that other add-ons have been experiencing as well. I know that Thunderbird Conversations implemented some complicated solution to partially solve the persistence problem, but a real fix requires that Thunderbird support a proper API to allow extensions to add columns. There is movement being made on the Thunderbird end to implement that, and I'm going to wait until that's finished before dealing with anything else column related. I don't want to do a lot of work on something that I know will change in the very near future anyway.
The checkbox was supposed to show up for the save button as well, but it looks like there was a bug in that function that was preventing that from happening. Thanks for catching that and letting me know! It'll be fixed in the next release.
-Jonathan