I originally posted this in the L3 forum, the work around is at the bottom of that thread.
http://community.logos.com/forums/p/10476/83557.aspx#83557
I am not sure whether the problem occurred when I installed Logos 4, or whether it was the update tool to get the resources from L4 into L3, but at some point the Andersen‐Forbes Phrase Marker Analysis and Lexham Syntactic Greek New Testament: Sentence Analysis were suddenly missing from Logos 3, even though the files were still there in my resources folder.
To get them back I had to flush the cache and update from the Libronix install CD.