In 3.x (and IIRC in earlier versions of 4.x), the JTAG port frequency could be entered either in full - e.g. 2000000 - or in abbreviated form - e.g. 2 MHz. After installing 4.05, I noticed all JTAG operations were taking *far* longer than usual to complete, and looking at the JTAG ICE Properties dialog shows why.
If you enter the port frequency in the abbreviated form, the 4.05 dialog ignores the frequency modifier part (the MHz bit), and just takes the numerical part as being the actual frequency. Thus, if you enter 2 MHz, exit the dialog and then open it again, you'll see your frequency setting now reads 2... Just something to watch out for in case, like me, you've installed 4.05 and are now wondering why your JTAG ICE is running like treacle on a cold day :-)