Ankle/shoe woes

I wonder if any of you ladies can offer any advice.
I'm developing quite substantial bruising/swelling on one of my ankles after riding.
It occurs on one particular pair of shoes - a new acquired pair of Specialized BG Comp road shoes.
I have the cleats set up exactly right, and exactly the same as on my Specialized BG Taho shoes.
The road shoes are great on, no problems, no discomfort, no pain or rubbing.
However, whenever I've worn them, I develop quite substantial bruising/swelling on the inside of my ankle on the right foot (left is fine), above the level of the shoe (it almost forms a perfect bruised outline of the shoe!), usually the day after riding.
I'm not sure what's going on, especially as they feel perfectly ok when I'm wearing them. I also unclip with my left foot first (at junctions, etc), so would have expected this one to be the problem if any.
I've checked the cleats and they're not misaligned.
I'm wearing them for long-ish rides (50-100 miles), but that should cause bruising/swelling, surely?!
Has anyone else ever had anything similar.
The shoes fasten with two velcro straps and ratchet/buckle, which I don't have super-tight.