Two things you have to look out for when you run a package from a SQL Server Agent job:
(1) Interactive components. Things like pop-up messages or user applications will fail.
(2) Permissions. When you run from BIDS, it runs in the context of your Windows login. When it runs as a job, it runs in the context of the SQL Server Agent service account (or proxy account).
You need to take the above into consideration when designing your package.