Total Fragments 99% and I cant get it to stay down
I have tried to rebuild the indexes as most of them are sitting at 99%. after the re-build they go to 0. but with in a few minutes they are back at 99%. 


I guess I know the answer here and have seen many times. Can you please check if auto shrink is on for the databases. You can use below query

select name,is_auto_shrink_on from sys.databases where name='db_name'


You must also check if there is any job running daily which is shrinking data file or may be shrinking whole database using DBCC SHRINKDATABASE command or may be using DBCC SHRINKFILE command.

Of course this could only be complete answer if you confirm whether any such activity is going on in database.