At the time I was dealing with the pain I definitely didn't think it was my boots... I thought it was something I was doing technique wise as well. I actually didn't put 2 and 2 together until the problem went away and I realized the difference was my boots.
It could definitely be something completely different including a technique issue... I'm surprised that Snowolf hasn't chimed in at all as he's usually all over any question about riding technique on this board. You may want to PM him and see what he thinks on this...