Sounds like the clutch is still hanging a little.
May be worth flushing the fluid all the way through.
***uming they've disconnected the driveshafts to remove the 'box, do you know what fluid they've put back in there? These Honda's can be a little picky apparently.
(Although I swapped mine out to a comma recommended substitute for the Honda MTF, and it got rid of my crunchy 3rd gear synchro)
It is of course recommended that you use the Honda stuff according to the manual, but my car's done 20k on something different and the gearbox is slicker than whatever was in it before.