What I would recommend in this case is check your Settings.ini file, as that is the only place of which I can think that something could be set causing things to be going elsewhere. By default, this should be located in the following path:
C:\Users\UserProfileName\AppData\Roaming\QlikTech\QlikView\Settings.ini
Use a text editor to have a look at the contents of that to see if you see anything related to log file location etc. If you do not want to really spend a lot of time here, you could simply rename the existing file and then reopen the client and reset the base settings and license etc., and then run things again and see if everything works as expected at that point. If it does, then that would confirm something was wrong in the old Settings.ini. You could try to see at that point if you can spot the setting that was causing the issues etc. if you wish.
Regards,
Brett
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