See if Honda knows anything about this, from
Edmunds.com:
Component Description:
5. POWER TRAIN: MANUAL TRANSMISSION Bulletin Number: 1205
Bulletin Date: DEC 2005
Vehicle: 2006 Honda Civic
Summary:
TRANSMISSION GRINDS AT SHIFTS, SKIP SHIFTING.
( NHTSA ITEM NUMBER - 10018868 )
My '06 EX coupe (MT) has a "notchy" feel when shifing from 2nd gear, into 3rd gear. (A "resistance," if you will.) I seem to notice it the most in cooler weather.
Regards,
Glenn in CT