I don't know about Your project, but I had a similar experience and after a while I realized that when enabling Flex mode for a track, all tracks with the same group setting/no will also be analysed...
My personal experiences with Flex lead me to believe that in order to fully understand how it does what it does and be able to use it to its full potential (and I don't by any means claim to have gotten there yet) you have to devote quite some time to learning all of its facets. Read the documents and keep practicing
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