Rev it up to 6500rpm+ and do a shift to see if it crunches. Then next time let the rpm drop to around 5500rpm and do a slow shift to see if it still crunches. If it doesnt crunch at the lower RPM then its pretty much normal behaviour for a GSR box. As Brian said its difficult to have a clean shift at 6500rpm+ without a slight crunch of some sort in 2nd and 3rd in one of these boxes, and it makes it even worse if its done a few km's and the synchros and hub and slider have some wear/damage.
Also 2nd gear is notorious for worn synchros and 1/2 hub and slider, keys and springs due to normal wear and tear plus people usually mis-shifting 2nd when they do some spirited driving. To change this stuff you need to open the box up and it aint cheap to replace with new OEM parts. It also depends on the type of GSR box you have as some came out with single synchro 2nd and others with double synchro 2nd gears or at least have been upgraded at some time to double synchros the same as the evo's had. Crunching into 3rd at high rpm is again most probably a combination of a single synchro 3rd gear and worn/damaged teeth on the gearset.
Ive included a pic to show you what a really worn slider looks like (broken teeth). Also is a shot of a worn synchro which has the teeth out of shape which will cause some misalignment when shifting.