When running with the -testnet option, I would expect the bitcoin.conf file in the testnet3 directory to be used, yet it uses the mainnet config file instead, yet the debug.log indicates the datadir is the testnet3 dir:-

2016-12-19 03:08:58.629380 Using data directory /home/rebroad/.bitcoin/testnet3
2016-12-19 03:08:58.629453 Using config file /home/rebroad/.bitcoin/bitcoin.conf