AxCrypt is really a very simple program in many ways (although complex inside regarding the crypto).
It does not do anything magic or particular with files. It encrypts them, making for example “Document.docx” become “Document-docx.axx”. It then also manages the process of opening and saving them in a relatively simple manner.
When properly installed on a computer, it will associate the “.axx”-extension with AxCrypt, enabling the right-click menu and double-click functionality.
The most common reason for this being broken is the user not fully understanding Windows file association, and reasons “I want this to open in Word, I will tell Windows to open it with Word”. There are many ways this situation can arise, but it’s the most common situation.
Another case might be when the user has downloaded the stand-alone “portable” version and never actually installed AxCrypt via the installer, which is required for Windows to be properly configured regarding the right-click menu and double-click.
The “file is in use” is most commonly caused by it being in use, often for example by the Windows viewer which refuses to release files. The cure is often to actually exit the program where it is open, not just close the document/file.
AxCrypt works well with most if not all anti-virus software, since it doesn’t do anything strange. It is in many ways very similar to compression and archive software such as WinZip and similar.