Key columns should have values that are (somewhat) unique to a given row, such as an ID number. Beyond Compare will give them precedence when trying to align your two tables.
For effective use of Table Compare it is crucial to set the right columns as your keys. The following table of sea ice thickness shows inappropriate keys and therefore poor alignment:
Sea Ice Data, with incorrect keys in the column top
By rightclicking the column tops we set the keys to a more unique identifier. In this case we chose date as the most unique key. In general, key columns should have values that are (somewhat) unique to a given row. Key columns are often independent variables rather than dependant variables. In the comparison below, date is the independant variable.
Sea Ice Data. Moving the key to column 2 gives improved alignment
Try it out yourself. Start a Table Compare session by pressing ctl-T and then click Table Compare. Or from the pulldown: Session->NewSession->TableCompare. Then browse or use your mouse to drag and drip two Excel files.
When the comparison loads, the rows might not align well. With the mouse, right click on your column tops to make them keys or not keys.
Don't worry: nothing you do will change your Excel file: it is read-only in Beyond Compare. And if you don't like what you do to the columns, you can undo your settings with the button at Rules->Columns->ResetAll.