New Instance missing Symlinks

I just started using this service. I have backed up my server several times and that seems to work. To test the backup, I created a new EC2 instance, but a couple modules weren't loaded in apache. I noticed the symlinks were replace with actual files in mods-enables. Then, I noticed the PDO wasn't loading with php - same problem. The conf.d symlink was replace with an actual folder. Now, I notice the mysql logins don't work.

Is there something I need to do different to make the backup/restore work?

Thanks!