I saw this somewhere but can't find it. Is there some information on whether checking one's backlinks, keyword saturation or ranking, for example, by using Marketleap's Tool, on a consistent basis will trip some sort of filter or SE problem? I think Jim Boyston may have brought it up, or Aaron Wall, but can't find the topic.
If you're doing it everyday, I could see the SE's asking questions. But I don't think it harms and I actually have never seen any valid proof that run these scripts will actually LOWER rankings.
If that program runs multiple queries to a search engine without following the SE's guidelines then it could create some negative effects. I wouldnt think that it would create negative for your website but rather the computer you are working on could be denied service or access to the SE that you are querying.