So I found that lookup tables are very picky. If they exist at an app level, they are only available for that app, no matter the permissions.
If you replace a lookup table, you must open the definition and automation and re-save them
One way to make them "less" picky is to put them at the system level, this makes them available in all apps. .. more info on that here: http://docs.splunk.com/Documentation/Splunk/latest/Knowledge/Addfieldsfromexternaldatasources
If you need to package the app, i found it necessary to add the lookup file/definition/automation to each app.
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