I have a similar problem to Bex who posted her problem up in June. Sorry to start a new thread. I also damaged my ankle ligaments about 18 months ago (they certainly take a long time to heal. Apparently the older you are.......) I have recently converted to SPDs (what a revelation) but with that, my ankle ligaments have started to twinge again. I have the SPDs on really, really loose, so there's no major movement in getting out of them. However the side that I tend to get off my bike is also the weaker ankle.
Could it be that this clipping in/out movement is causing the pain and stretchy feeling of the ligaments (funnily enough I can walk realtively OK and when exercising the pain goes, but comes bank with a vengeance afterwards?) Someone also told me that that very action of pulling up may also be causing the pain and stretching.
Any advice (other than what you told Bex, and training myself to clip out of the other foot?)
Many thanks