No, but let me know when you find out. I've had my A6 since 2005 and 137k miles and neither oem key fob will pop the trunk. Same thing as yours -- I can manually unlock. The push button on the inside of the driver door frame does not seem to work either.
2011 A4 2.0T MT6 (120k)
Premium Plus; Colgan Bra
2003 A6 2.7T MT6 (240k) - SOLD
Premium-Cold Weather Pkg
GIAC-Bailey DVs-Samco TBB-K&N
AWE Stage 2 Clutch+Lightweight Flywheel
Billy Boat Downpipe Kit; SS Brakelines