I have had no problem running the packages directly from the agent from the file system  by simply selecting SSIS package from the drop down and filling in the package path. ...

Here's a tip: don't use the annotation feature.  I foolishly thought it would be a handy way to record package changes and relate them to software versions and bugs.  Turns...

what happens when you open the package in designer, go to package properties and change the protection level from there?

if you want to execute the package via the agent you have first change the protection level to DontSaveSensitive or EncryptWithPassword (This is in the package properties). The default is EncrypWithUserKey...

What I do is create a sql task that contains a query that returns 1 or 0 based on the condition I want to test for.  Store the result of...

The agent can't run an ssis package unless the protection level is set to "dontsavesensitive' or 'encrpytwithpassword'.  If you change the protection level you lose the saved passwords and you...

I get your point, and feel your pain, regarding the subject of over-normalization.  However, that being said, you picked a bad example of the genre.  I can think of several...