Try doing it like this:
factom-cli newaddress fct bitcoinsandiego "12 words from koinify inside the qoutes"
factom-cli newaddress fct bitcoinsandiego "12 words from koinify inside the qoutes"
that's exactly what i've done multiple times
The S error is a bad wallet. I had one after the first binary release. I closed either the factomd or fctwallet be ending it instead of ctrl-c or it was a power outage. I do not recall what killed it. The updated release fixed it for me.. It is (was) possible to mess up the wallet. With the update, I believe the wallet was 'fixed' also. Are you using your backed up wallet every time or have you tried importing your 12 words to a new wallet?