Calibre (or any other program) will NEVER uninstall itself without user specifically initiating the uninstaller.
You may have a rogue Antivirus program that is removing key parts (not the same as a true uninstall).
A true uninstall, cleans up all Program files (there may be a folder left because of patches/updates). There will be NO exe or dll files in the calibre2 folder (if it still exists in the Program Files location.
Please report back which what OS (on a 32 or 64 bit CPU) and which security software. include the name and version