Every manual I've owned has behaved like this, including 3 Tacomas. It's never been frequent, maybe once every couple months or so. I've always just assumed it was an operator error like not having my foot down all the way.
I have had this same experience of the first gear syncros not being great until you're completely stopped.
Also not to hi-jack but is anyone else trying to start in 2nd gear more? It is nicer because of the terrible ratio jump but don't know if I'll eat up the clutch....