test usb functionality from the handset? I am using HTC Desire HD, I have a terminal with root permissions.

Are there any tests I can do on the USB port from the handset side?
i.e. to make sure it exists and is functional.

The reason I am asking this is that my computer (Windows 7 64 bit) does not recognize my phone when connected,
however it did recognize another phone of the same brand (but with a different rom).
This sounds like a driver issue.

You should be able to download the HTC Sync for the desire HD and it should include all the system drivers you need to connect to the device.

I am thinking driver because if you have the drivers for "Google Experience Devices" installed on your system already, and the other device is running an AOSP ROM, like cyanogenMod for example, then the android sdk drivers will work with that ROM. The other device, that isn't recognized, is running a non-AOSP rom, it will require the manufacturer drivers for the device.

Again, I am just guessing since I am not sure what ROMs you are running, or what PC operating system you are connecting the devices to.