albert,
I found this a neat an interesting problem but I haven't had a chance to try out my idea. I do have a couple of questions first:

• Do you need the count breakout per position or just total over all strings?
• With 010 and 101, should the count of "01" and "10" be 2 per position for a total of 6? In other words, do each strings need to be compared twice taking turns being on top?

I don't think any answer to the questions would invalidate my idea but it might change the implementation a bit. Since I do not have time to try it myself, I am laying it out here.

I believe you should be able to mathematically determine the counts without doing the comparisons. I believe all you need to do is count how many 0s and 1s there are for each position. To further speed up the process, I might even consider doing the counting using Inline::C.

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