Honda's TSB finally issued on the 6-speed. Thanks to User EZshift5 for the update!
Honda TSB 08-020 April 12, 2008 Transmission Grinds When Shifting Into 3rd Gear, Pops Out of 3rd Gear, or Is Hard to Shift Into 3rd Gear SYMPTOM The 6-speed manual transmission grinds when shifting into 3rd gear, pops out of 3rd gear, or is hard to shift into 3rd gear. NOTE: These symptoms can be intermittent and sometimes more noticeable in colder climates. PROBABLE CAUSE The transmission has a faulty 3rd gear synchronizer or 3-4 shift sleeve. CORRECTIVE ACTION Replace the 3rd gear set. VEHICLES AFFECTED 2003–07 Accord V6 with M/T: ALL 2008 Accord V6 with M/T 2-Door: From VIN 1HGCS218.8A000001 thru 1HGCS218.8A003478 2006–07 Civic Si 2-Door: ALL 2008 Civic Si 2-Door: From VIN 2HGFG215.8H700001 thru 2HGFG215.8H701973 2007 Civic Si 4-Door: ALL 2008 Civic Si 4-Door: From VIN 2HGFA555.8H700001 thru 2HGFA555.8H702465</span></span>