Check your bios to make sure that you (or someone else) haven't disabled any cores, although exactly how you get "3" is a bit weird... With the same software my 6300 shows 6 cores/threads.
However, technically speaking, the 6300 has three modules, and those modules have 2 cores each. 8xxx series has four modules, 2 cores each. Some software, like the Heaven and Valley benchmarks, count the modules as cores, and show the 6300 as having "3x" in the results posted after a benchmark run.
In the bios of my MSI G46-970a, it's possible to enable/disable modules 2 and 3 (but module 1, of course, is always on.) Ergo, in the FX processors you enable/disable cores in pairs--you cannot disable individual cores. Perhpas for some reason your version of cpu-z is counting the modules instead of the cores--but I've never seen that happen for me, and that's why I recommend you check your bios.
Win8.1 x64, UEFI install, version 2.6
FX-6300 @4.5GHz, stable, Turbo disabled, C&Q Enabled
8-gigs 1600MHz DDR3,2x4, 225fsb, 1800MHz effective, 1.5v
Boot: Seagate 320GB; WD 1TB Blue;2x500GB Barricudas=1TB RAID 0
Radeon HD 7850 2Gig
Lian-Li PC-V1200 case
Corsair 600W PSU, 1x 49a 12v rail