According to the CIC encyclopedia, the Trafalgar and Wolfhound were Bengals while the Gettysburg was a Waterloo.
EDIT: The Gettysburg is apparently the same ship as in SO1.
The TCS Trafalgar that is listed in the CIC Encylopedia appeared in the sixth episode of the Wing Commander: Academy TV series ("Chain of Command") where it was destroyed by the Kilrathi. This took place in 2654, so the Trafalgar from End Run can't be the same ship.
This most definitely says "The Trafalgar was destroyed during the battle at Vukar Tag in 2667."
I believe End Run specifies that the Trafalgar is a "CVA"... whatever that is.