Hmmm, they are not going to cause that problem. There are some CAI on th market that clash with the transmision in the engine bay. Could be a selector issue, a known issue with this box.
Never heard of this one on a Honda but had it with my old Corrado - Never really found out what that was cos a straight gearbox swap (old and less hassle to replace than strip out) sorted it immediately. Sorry can't be more help...
Yup, had that problem on my car when I was using Redline transmission oil (race spec, color coded blue). Apparantely, it was too 'soft' for the gear box. Changed it out and now it's ok.
I'm not sure if it's the same as the civic but I've heard that there are some inherent problems with the DC5 gearboxes. Some folks have problems with it here in Singapore. What transmission oil are you using? If you changed it out before, you might want to go back to Honda MTF V2.