Are you using version 2.1.1526 ? This was a version that was available for about a day, which included a serious reliability issue which can cause what you describe under certain circumstances (notably, files left open when AxCrypt was automatically signed out). It was withdrawn very quickly.
If so, you would have received a pop-up message stating you must update because of this. We have a mechanism where we can flag specific versions as “bad”, either for security or for reliability. As long as you allow AxCrypt to connect to the Internet, you will be prompted to upgrade in very strong terms.