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Do these files get modified in the meantime? "Modified" means that either their contents change or their modified time. Check with an (S)FTP client application or with your site's hosting control panel. If the size or date of the files changes every time then they are, indeed, modified every time which would explain why they reappear.

Note: I assume that they are reported as modified. This column of the report, like all other columns except the filename, are not included in your screenshot so I have to make assumptions. If my assumptions are wrong please send me a screenshot with all of the columns.

If the files are marked as Modified it means that they have changed since the last time the scan took place. When the files change the Mark As Safe flag is ignored. Remember, Mark As Safe marks files as safe until their next modification. A file is considered modified when either its contents or its last modification date has been changed since the last scan.

Considering that these files belong to the JoomlaArt template you should ask JoomlaArt why they are constantly modified.

As far as Admin Tools is concerned, it is correct in reporting modified files as such. The full name of the feature you are using is PHP File Change Scanner. If a .php file is changed it's meant to be reported. That's the whole point of this feature.