Hello Kong77,
There is nothing wrong with the way your computers are set up. The one with the files showing that begin with periods (".mozilla", ".gimp", etc.) just has the file manager set to "Show Hidden Files". Open the file manager and hit "View" along the top to see what I mean.
Files that begin with a period are "hidden" files. In your home directory those are usually program configuration files. For example, the ".mozilla" folder holds any customizations you've done for your Firefox browser (bookmarks, cookie settings, addon settings, etc.). As you use programs and change settings to your liking, the program configuration files hold those customized settings. They aren't normally files that users need direct access to, so they are hidden to make it easier to quickly see and access the files that you do use all of the time -- Documents, Music, etc.
If you use LL on more than one computer, rather than going through the trouble of making customization changes to your programs separately on each, you could just do it once -- then simply copy the hidden config files from one computer to the other and instantly have the second customized the same way.
A lot of people do periodic backups of their entire home directory (including the hidden configuration files). If something happens to the system requiring a re-installation, they simply copy back the files from the backup and have not only their data, but the programs configured the way they had them before also.
