Would it be better if application saves LOGS into native system?
If so, you need to change isolation mode in your ThinApp Project. Look into ThinApp project, go to directory %ProgramFilesDir%\ensembleProAgent\LOGS\ (just create it if it doesn't exists) and create file in it called ##Attributes.ini with following content:
[Isolation]
DirectoryIsolationMode=Merged
Rebuild project and your log files will be created on native system instead od sandbox.
Have a nice day,