Mac App mysteriously remembers deleted settings

After evaluating several its demo version, I decided to buy Linkinus from the Mac App Store.¹ As I had played with the settings a bit, I wanted to do a clean reset before seriously using it.

So I deleted all preference files and folders containing with the app's or its developers's name from my home directory, which were:

~/Library/Application Support/Linkinus 2
~/Library/Caches/net.conceited.Linkinus
~/Library/Preferences/net.conceited.Linkinus.plist
~/Library/Preferences/net.conceited.LinkinusSysInfoPlugIn.plist

To my surprise, Linkinus still remembered at least a part of its preferences after relaunch.

So I dug deeper, reinstalled the app and also deleted:

/private/var/db/BootCaches/XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX/app.net.conceited.Linkinus.playlist

As that didn't help as well, I tried to deactivate iCloud – also without success. I even used fseventer to take a look at the files read and written while using Linkinus, but that also didn't give any additional insights.

Can anybody solve that mystery?

¹ Yeah I know, the developers appear to have disappeared for a while, but I still like the app.

The app is pefectly innocent, this is an issue with preference caching on Mavericks.

What finally worked was running defaults delete $app_id, so in my case:

defaults delete net.conceited.Linkinus

Source: Deleting plist file does not reset app on Mac OS 10.9 Mavericks on StackOverflow