As F.J. notes in his article, Filefault mounts a disk image for your home directory, this means that your home directory is not longer truly located at Users/username but is instead a volume mounted at that directory. You can see this using two accounts and fast user switching. Log into the account with Filevault on and switch to a second account, you will see a link in the Users folder for the account with FileVault. Then switch back and log out of the filevault account. Then from the second account, you will see a folder in the User's folder with the disk image in it.
Even when looking at your own home directory, you don't see that there is this link there, your script is running into this unix link and does not know how to follow it. There are ways around this, but it is hard to give you answer without know more about your script. Please post at Apple's discussions if you would like assistance.