Hello Mike,
AxCrypt app will encrypt most of the file types. Also some file types AxCrypt will not encrypt due to security reasons.
AxCrypt will not encrypt any system, hidden files and operating system installed drives/folder. So please avoid securing that kind of folders.
It may be the file is hidden state. So check the file properties the file is hidden state or not? If hidden the file means, Please remove the access, then to encrypt the files.
If you are receiving the warning dialog frequently, please click the Don’t show this again option. After that you never see this kind of warning.
Still, you are facing any query, please provide detailed information about the issue and write a mail to support@axcrypt.net. We are happy to help you.