I agree, I've had the car for 5000km
The problem is getting less and less frequent
maybe its just me adjusting to how I drive the car
It seems this habbit has been built into the honda gearbox since forever
Talking to other honda enthusiast driving EG, Ek, DC2/5s. They all have their own little quirks with their gearbox.

Took the FN2R to the track over the weekend, got an instructor to drive it.
http://www.sendspace.com/file/tc3zdw
He didnt miss a beat. In fact he was utterly amazed by the quality of the gearbox. Hence from this day forth, I shall never ever complain about 3rd Gear ever again ahhaha