I've noticed that in recent versions. I think that all the lists - filters, templates, sorts, lookups, summaries - behave the same way, and if I'm not mistaken it's all on the order each object is created. So the first filter you define will always be at the top of the list.
A crude hack would be to duplicate your filters in the order you want them o appear, and then to delete the originals. I'd suggest backing up your model first.
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