What are you trying to accomplish by doing this? I can't really answer without knowing, but I'll guess anyhow.
If you are mapping something that was recorded without a click, then all Logic is doing is displaying the tempo between each beat you have mapped. I don't believe there is anyway to force the mapped audio to a constant tempo within the same project, but I could be wrong.
If you are doing this in order to force the non-click recorded track to match to something that is on a grid, I think you need to map the audio in a separate project and then export the audio file. Logic will include the tempo and beat map in the file. Then open up the project you want the file to conform to and drag it in. Logic will ask to import tempo info - say NO. At this point, if you click flex in the inspector, and then choose polyphonic and check complex - it should snap right up.
I am assuming you have a destination in mind for the audio, but this would also work if you just want to start from scratch with something and import into a new project afterwards.
Let me know if this helps! There is a Steve H TNT about this (that's how I know how to do it). He explains this infinitely better than I did!
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