Frequency of StratixIV

Your screenshots are extremely hard to read. From what I can decipher in the sopc shot, the CPU clock is 50MHz. Does it show 100MHz in the clock list when you change the setting in the pll component?

In the RTL view you should find the pll inside the sopc block, several levels down in the hierarchy.

You have lots of printf's in your code. This is typically an I/O operation than will take some time, even with a fast CPU. You should have a loop without any I/O between your two clock() calls if you really want to see a difference with a faster clock.