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I have a wireless USB keyboard/mouse combo (Microsoft Wireless Keyboard 1000) which is working perfectly on a 2013 MacBook Air running Yosemite, the keyboard & mouse work perfectly - but only when the USB receiver is plugged into the right-hand USB port.

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When it's plugged into the left-hand USB port it doesn't respond to the mouse or keyboard at all. The left-hand USB port works for other devices such as a USB hard disk.

So, the left-hand USB port is working, and the keyboard/mouse is working (including on a separate MacBook), but they're not working together. This is a pain due to the configuration of my desk, otherwise I'd just live with it.

I've tried resetting the SMC and NVRAM but this has no effect. Any ideas for how to debug this further?

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You can look at the USB device tree using the System Information application, launched either from the "System Report" button in the "About this Mac" dialog, or by looking in /Applications/Utilities.

Select usb from the sidebar and it will display the device tree. See if you get different information when you reconfigure your devices.

Also look in the system log (via Console.app also in utilities) to see if there are any messages when you change your config.

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