So, I've had this happen in another vehicle of mine. It ended up first being the transmission fluid that was used. It was breaking down too quickly and was causing a grind in 3rd and 5th gear. I changed the fluid to something a bit better and the grinding went away. Fast forward about 9 or so years later, I started to get a grind in 2 gears again. I knew it wasn't the fluid and was the synchro's this time around. Had them replaced and the grinding is gone. Not saying your issue is the fluid, but it may be a place to start. Knowing your mileage, this may not solve your issue though. Just some input from my experience, but hopefully others might chime in with additional input for you.
If you decide to tackle the fluid first, this might help you:
Porsche Boxster Differential / Manual Transmission Fluid Change - 986 / 987 (1997-08) - Pelican Parts Technical Article