For some reason when I view system information in Windows 7 it will only display the stock clock speed of 3.39, but both CPUz and the BIOs show it running at 4.5ghz, is this just a Windows bug?
That's not a bug, just a feature. Windows is simply reporting what the stock capability of the chip is. The intent of the "system information" is not to monitor performance but to tell you what hardware/software is installed. The design frequency of the chip is 3.9GHz, so that is what is reported.
Don't listen to Windows... CPUZ is reporting correctly. If you are still not convinced it is running at 4.5GHz then run a small benchmark at stock clocks and then overclock to 4.5GHz and run it again and see the performance jump.
If you overclock manually, Windows 7 will report the true clock speed, i.e Core i7 2600K 3.4 ghz 4.50 ghz. If you overclock using auto settings, it will show the 3.39 ghz instead
Either way, it doesn't matter since the overclock is still there