I have had the car for a couple of months after trading in a '01 Maxima SE 5speed. The only thing that bothers me, and was exactly the same issue on the Maxima, is a fuel cut issue. To explain, if say cruising along at a constant speed in 3rd gear and you imperceptibly back off on the throttle, the car goes into a fuel cut mode for emissions control. The problem is that it is impossible to re-establish the throttle without the car jerking. With the Maxima I was able to find through a similar forum that there was a programming change available that helped lessen the problem. After much hassle and denial from the Maxima dealer, they finally made the change and the car was better. Is there similar experience out there from other 5 speed owners and is anybody aware of a similar solution to the Maxima?

 

I've got the same car, a 4-door version. I've not noticed anything out of the ordinary with my car. The symptoms you mention will be more noticable in the lower gears, especially 1st and 2nd. Third gear, to me, is high enough that this isn't that much of an issue, at least on my car.

Honda put a DBW (drive by wire) system on these cars for mileage and emmissions reasons. I'm finding that I'm not impressed with the feel of the system. I find it "extremetly" difficult to modulate the throttle while shifting gears. The system does not feel consistant in how it reacts to throttle blips to rev match on downshifts. It doesn't release the throttle immediately on upshifts, which isn't a big deal in normal driving but becomes a bit PITA when I'm on the car a little harder, shifting in the 5-6k rpm range.

I'm happy with my car overall but that DBW system does have it's quirks. I'm betting it's the cause of your issues. The '06 Civic is a new design for Honda. I'd be surprised if they've got any kind of reprogram for the car yet but I could be wrong. Please let us know if you fine out about anything and I'll do the same!

Good luck,
Steve R.