This is the default structure for Visual Studio projects. A project is developed in the User's Documents folder to keep them separate from other users on the computer. Debugging is done from the folder that was causing the problem. Once the application is finalized, the application .exe is built in a Release folder and the installer installs the release version on a target computer in a structure defined by the developer. I routinely install in a subfolder of the Program Files folder. User specific input and output data from the application is stored back in a subfolder of the user's Documents folder to keep them separate from the data of other user's and to assure that they are backed up by normal backups.
BTW, the problem has stopped occurring. I suspect that the change of Detection Engine corrected the problem. @Marcos has not verified this, though.