Paxton had already paid a $1000 fine on this, I believe, based on a technical infraction.
Then after the SCOTUS ruling, he issued a statement that no state or county employee would be fired for refusing, based on religious belief, to issue marriage licenses to gays.
Now this.
No, that was a different offense, "failure to register" as an investment advisor, with that fine being levied by the Texas State Securities Board.
Haven't read the indictment yet (haven't found a copy, still searching), but from news reports, it reads like "fraud."
Bam. There's your probable motive.