I ran into this issue yesterday when we were loading the package spec. It said that everything loaded correctly but when I went to look for the specs that were listed in the package spec they were nowhere to be found. Come to find out some of the catalog assemblies were incorrectly cased. So we changed this
and reloaded the package and everything worked as planned. Notice the CustomFX to CustomFx. We are using SVN and I was told that things in SVN can be case sensitive.