There are a few other items we can look at, the other things that come to mind are permissions on the lookups themselves both file system permissions and meta permissions. The default.meta that ships with the TA exports almost everything except the commands, it should look like:
#shared Application-level permissions
[]
access = read : [ * ], write : [ admin ]
export = system
#This is a TA, so export almost everything
[]
access = read : [ * ], write : [ admin, power ]
export = system
# Do not export commands
[commands]
export = none
Also does the process running Splunk have the proper permissions on the lookup files?
Lastly, can you look at the lookups settings in Splunk web - in a fresh install the sharing permissions are global.
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