On slower rpm shifts, the synchros are spinning faster than the actual gear speed so you are basically jamming it in there. Whereas, on higher shifts, the speeds are more in sync so it is smoother. When shifting at slower rpms, try waiting for a second out of second gear before throwing it into third.

 

I had a problem shifting into 3rd with my 04. I've found the best way is to guide the shifter into neutral, then guide it into 3rd, aiming just slightly to the left of the front center of the hood. Try this and let me know if it works.