Let me start off by saying that I'm extremely rusty with regards to JAMF integration.. And I must admit that I've not tested an indexed package (or any package) in a couple of years.. I know that App Portal requires an indexed package to support install/uninstall, so there should be no problems.. To me, based on the output, it sounds as if not everything had been cleaned up after you first added the package prior to indexing.. The status - conflict, seems to imply this anyways.. I don't suppose that you would have another indexed package handy, which you have never added before though App Portal, to see if the same behavior persists?
Kind of funny, but I went to test this quickly, and the first thing that I saw when adding a package was the identical error to what you were seeing.. I ended up deleting the package, changing the title of my catalog item a bit, and did not see the behavior again.. I don't believe that my package was indexed... Try deleting the package, and changing your catalog item title.. Also be sure that there are no static computer groups or policies (I think that is what they are called) already in Jamf for the package (at least those created by App Portal).. Finally, try restarting the ESD Service, as I seem to remember there were some items which get cached in memory which might cause some strange behavior.
