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Sorry I wasn't very clear - the first count is what you get summing all the countries reported, including the UK. The second count is what you get summing the UK county totals (so should be the first value minus expat votes). The headline reported total is bigger than the sum of all country votes by about 1.5 million - 2,783,605 vs 1,311,334 at the time I downloaded the data.
They may have caching issues between the two counts (one calculated out of step with the other).
More likely, they may have locations / postcodes which they're not mapped into a constituency (we were looking for the Isle of Man on their hexmap yesterday and couldn't find it for example). the counts are within 5% of each other