In the settings, the Testnet seems to be reading from and setting some options for mainnet and not testnet. I have noticed this with at least the strDataDir option.

Replication steps on Ubuntu 15.10

1. Tail ~/.config/Bitcoin-Qt.conf and ~/.config/Bitcoin-Qt-testnet.conf
2. Reset the testnet settings by going to Settings > Reset Options. Notice how the testnet conf file changes.
3. Now start Bitcoin core with -choosedatadir -testnet.

After the third step, you will see that the strDataDir setting is not added to the testnet conf but is added/changed in the normal conf file.