Mac – How many USB buses do Mac Pros have

It seems that those after 2009 (which reverted to 4 USB ports instead of 5), only have 2 buses. The 2009 models are likely the only models with 3 USB buses.

If you get one of the newer ones with Thunderbolt, it's possible to connect to a Thunderbolt Display which would add a third hub. I don't know of any devices off-hand that will give you just another USB hub via Thunderbolt, but if they're not out there already, they're bound to show up.

It's difficult to tell if you have a hardware issue or this is just how things are designed.

Have you read through this article on how Apple detects the first device that requests higher power and enables that power on some, but not all ports?

• Apple Computers and Displays: Powering peripherals through USB

I know you have linked to it, but the 500 mA is subject to measurement errors on the computer side - so plugging in a device can draw more current than the device says it should. Similarly, the measurement side where the Mac determines the actual power draw could be flakey or failing. This sort of thing isn't tested in the system diagnostics. You would need a test set / oscilloscope / engineering lab to really measure these currents with enough resolution to pin down exactly what is happening.

It could be just the order in which the system decides to detect a device attached. Once you have ruled that out and have a repeatable issue - you might need to have the Mac checked for service if it isn't producing power as expected. Now that you know that the order in which devices are plugged can affect things, perhaps this will help narrow down if the enhanced power is correctly available to some (changeable) subset of the ports and hubs made by Apple.

There is no easy answer other than being precise and narrowing down exactly which devices are causing errors and statistically determining/isolating whether it's the devices or the port that is out of spec and needs to be replaced.