2 answers
Can't find the exact reason why, it happens to be the way Pardot is set up.
Will be interesting in seeing what others think, but Pardot documentation only seems to affirm that "each open is counted separately". It could certainly have something to do with the way the emails are tracked to begin with.
Most orgs I have worked with love this. The downside is, of course, some sophisticated spam checkers trigger multiple email opens when they scan an inbox, which results in absurdly high scores for some prospects.
For those who don't find as useful, @Tom Bassett 's solution above is the way to go.
