I believe the noise you're hearing is because of the clutch being out of adjustment or in need of a new clutch.

Adjust your clutch (free play) properly with the bolt down on the clutch pedal.

Ours' did the grinding noise, especially in the higher gears.  I would have to throttle ~way~ down, be at a complete stop, then put it in gear.  That was my best way to get it to go until we had a new clutch put in.

I dont think it is the transmission thrashing...it's just not getting in gear/grabbing the gear properly.  Adjusting your free play will help some.  If you're out of free play, then send it in for a clutch job.