When inserting a backup, the Swap Magic software starts to read the disc. The Swap Magic software uses colors to tell you if something is wrong, and if everything is OK. 
Blue: The backups is OK, and ready to boot. The game should work - if not, there is simply no way to play that particular game using the Slide-Tool. You will properly need a Magic 3.1 mod chip to play that game.

Green: The backups is OK, but Swap Magic is having trouble reading/understanding the disc but goes ahead anyway. If the game plays, then ok.. If not, the most common problem is simply the use of bad quality CD-R or DVD-R media. Copy the backup to a better disc, and it should work. This is a general problem with all backup solutions. People are not using good quality media. 

Red: Swap Magic cannot read the disc, there is no way this disc is ever going to play. The most common problem is the use of bad quality CD-R or DVD-R media. Try a more expensive brand like Verbatim Data-Life. More common is the game not having been backed up properly. You need to use a different method, different software, different CD/DVD writer etc. Look in popular PS2 Forums for help making backups.