The "Try not to tag compilations" Preference check box is an advanced feature within TuneUp. It is located within the Clean tab within the Preferences window.

First, it is important to understand that in this context "compilations", means "artist compilations", such as "Greatest Hits", "Essential", and "Best of" albums, where all of the tracks on the album are from the same artist, as well as "Various Artist" compilations such as soundtracks, tribute records, or "genre samplers" like "Best of the 80's" and the like. 

Since a recording of a song can be on more than one album, the audio fingerprinting algorithm that identifies the music may not be enough information to identify the exact album, which is why this setting exists.  If we aren't sure, then this setting essentially tells us your preference of either the "original" album release or the appropriate compilation.  NOTE**: The more tracks from an album that we search for at the same time, the more accurately we can identify the correct album.  This is why we suggest that Cleaning by artist is a good method for insuring accuracy.  See: Step by Step: Cleaning Your Entire Collection for more info on this.

• When the box is "unchecked", and TuneUp searches on multiple songs in a users collection that belong to a "compilation", the results returned will assign these songs to that compilation.
• The example below shows what happens when I show TuneUp 5 tracks from "The Cars: Complete Greatest Hits." TuneUp suggests "Complete Greatest Hits" as the album for all 5 songs