We were discussing this just last night in chat.
Basically, by submitting your score from multiple places, you can end up in the top50 multiple times. This isn't looked too kindly upon by the community (when done excessively and purposefully, of course). I do believe it affects the in-game t50 ai, but don't quote me on that.
Because the list is hosted by Mochi, I don't think there's really much that can be done (as smug said, there are more important things for them to worry about... such as proper flash compatibility -ahem-...) A more viable solution would be to code a new highscore table independant of Mochi. However, that would take time and effort on Zanz's part, and I'm sure he also has more important things to worry about at the moment.
Right now, we can really only ask that people in the t50 please try not to submit scores from many different multiple places, for the sake of common courtesy.
^This. And in case anyone needs reasons as to why this should not be done, I'll compose a list for you.
1) The rare card farms list. I personally must applaud whoever takes the time to modify that spreadsheet because I wouldn't have the patience to keep changing everyone's current deck, especially when the same person logs their position in multiple times. Notice that the same person's ign appears only once on that list, which means that this once useful tool is practically obsolete and the process for updating each deck on that list has now been made several times more difficult.
2) Farms. I understand that there are some people in t50 who could care less about putting up farms for other players, but for those of you who do, this causes a potential problem when trying to find a farm which meets the needs of the community.
It's true, you can have several different farms up when resubmitting your position, but does this necessarily mean that every single rare will be accounted for by doing this? There are several t50 who have been knocked out of the list who used to take farm requests regularly; this latest scheme has the ability to be responsible for breaking down this system.
3) Other t50 members. For several players, t50 is seen as a major achievement and a way to finally give back to community. Can you imagine how infuriating it must be to have your rightful place revoked simply because someone felt the need to make him/herself the best in 3, 4, 5, or even 6 places? This isn't just humiliating or disrespectful, it's essentially dehumanizing and needs to stop.
Though this may not be a prevalent issue, I thought I would mention that because this is basically a loophole in the game's highscores, this is also an exploit in the game itself. And as history has shown us, abusing these loopholes are never a good thing; I am personally requesting that from here forward no one speaks of how to exploit this loophole. It's caused enough trouble from mentioning it once, but to repeatedly speak of it increases the chances of the top50 becoming the top10 or even just top1.
Now, I don't know why this has been done and I won't ask, but I find it difficult to be believe that this scheme has been done for the good of anyone except the user him/herself. Reconsider doing such a thing in the future in order to preserve the dignity and respect from the rest of the community if you would please.