First of all – actually 2.1.1398 is the most recent version. It addresses an issue with how files are handled, but typically you’d see an error message if you had that problem, and it’s been very uncommon.
I’m a bit surprised about your descriptions – we’ve really not had any reports like yours. There has of course been issues, but typically they will result in an error message. I would really appreciate an snapshot report as I described above. It helps understanding what has happened.
I’ve not seen or heard of any problems with file-name collisions or special names. Collisions are supposed to be handled gracefully, either by renaming automatically, or by asking the user depending on the situation. I just tried the scenario with an existing clear text – a dialog is shown asking you to ‘save as’. Perhaps you did not notice this dialog?
The two error messages at the end are not good though. They indicate file corruption. This is typically irreversible. The first one is hard to say, it may also be that you have renamed a file that is not an AxCrypt-file. It should display the name of the file of course, that is a bug. Did you restart the computer or something while the encryption was running? The second message seems indeed like a file that was only partially encrypted and then the computer or AxCrypt crashed. In either case, there should be backup-copies available in the folder (named .bak). Otherwise, I sincerely hope you have backups, although I have the uncomfortable feeling the answer is no.