Are you using the correct cables. iPod cables look similar, but are not, as they are 1.1 USB cables, where your iPhone and iPad require a 2.0 USB cable.
Also, make sure you are not plugging your USB cable into a Hub or keyboard USB port, but one directly on the computer.
You may want to reset the USB ports, by resetting the SMC and PRAM
HT1379 About NVRAM and PRAM - http://support.apple.com/kb/HT1379.
I took my iPhone and Macbook pro to the genius bar for this problem. When they used their cables, it synced flawlessly, I realized that they changed the way it looks when devices sync into iTunes. There's no icon on the desktop, and there's no evidence that the device connected, except for a new button on the top next to iTunes Store thats hard to spot.
I admit, I'm not as familiar with Apple devices, but I know what it looks like when an iPhone syncs with the previous iTunes. Is it possible you're just missing the icon in the new layout?