You may want to look into the differences between the "!=" and NOT (XXX) searches. There are some intrinsic differences, and its probably why you are seeing some oddities..
As Lisa says, your search is inefficient... I would recommend adjusting..
index=myindex NOT (source="WinEventLog:Application" OR source="WinEventLog:Security" OR source="WinEventLog:Setup")
Here is some more reading on similar topics:
https://answers.splunk.com/answers/43228/use-of-not-vs.html
http://docs.splunk.com/Documentation/Splunk/6.4.0/Search/Usethesearchcommand#Difference_between_NOT_and_.21.3D
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