I'd noticed occasional delays in the lights switching on as I walked around. Not serious, but noticeable. It wasn't entirely clear what was causing them.
After moving back into the main bedroom I needed to change some configuration, so logged into Cortex via Remote Desktop as usual. The response seemed to be a little sluggish, not how I remembered, to the point of being difficult to use. I have switched recently, but the Apple remote desktop client seemed OK when I first tried it.
Since there haven't been too many updates to Cortex recently it wasn't obvious what was going on. Eventually, I checked out the disks with the disk management tool and discovered the C: drive was massively fragmented. It took quite a while to defrag, but afterwards the machine was back to it's normal GUI performance, though it's too early to tell whether this will have eliminated the lighting delays.
Admittedly I do leave Cortex running with quite aggressive logging, so many small files are being created. I don't want to have to remember to perform regular maintenance, so I think I'll be installing Diskeeper to keep a lid on fragmentation in the future.