When I go to say analyze a playlist that has 540 songs in it. MIK initially shows it has 540 songs when you click the add file button. However, MIK will only analyze in my case 516. I tried to re-analyze the playlist and even remove it from the collection. Now MIK won't re-add this playlist to my collection. Any help would be appreciated.
There could be some broken filepaths in your iTunes library, it would still count those files as part of your iTunes collection but they wouldn't be added to MIK since the filepath would be broken. If you select all of the files in iTunes and drag them over to MIK it will skip the already analyzed files that exist in your collection and if it was just a glitch that they weren't originally added to MIK's collection so that would be your next step. Other than that I would try to locate a few of the files that aren't part of MIK's collections and try to figure out what is different about them compared to the files that were added.
Let me know if it helps :)