The TT must first be on, and second the TT itself needs to recognize that it is plugged into windows whatever OS you use. Only then it will ask to be connected to your PC then Windows will recognise it.
USB ports first go through a USB controller then to the motherboard so it does not matter which one you use.
You must check to see if you TomTom is charging off the USB connection, then probably your USB connection is correct and it may be the faulty tomtom software.
If you still get no joy, try downloading and burning an Ubuntu disk. Ubuntu is a free Linux operating system that will allow you to boot and run it from the cd (it will not affect your existing Windows installation, you just select 'run from cd').
Once you have booted into Ubuntu you can check to see if it can see your SatNav. If it can then the USB interface is working perfectly on both the SatNav and your PC and it is then just a software issue (USB driver and/or the TomTom Home program).
I think the original creator of this thread has solved his problem long ago since it was started in January, but for those reading this to find a solution to a similar problem I recommend the previous idea re: creating an Ubuntu disk. Sometimes windows can 'ignore' some USB devices if there is a conflicting driver; Ubuntu will let you see ALL connected USB devices regardless of whether it has successfully installed a driver for the device or not.