I am in the process of setting up Paratext and FLEx for three languages. We are about to start working with all three as part of a cluster project.
Since we already had some dictionary data from Shoebox, we began by importing that data into the FLEx projects. Then we tried to associate the FLEx project to Paratext via Project properties > Associations tab. After selecting the correct FLEx project for that Paratext project, we got the red circle error. The helps say, "If a red circle appears, it indicates that the language identifier in Paratext is not the same as the language identifier in the lexical project you selected." However, we have confirmed multiple times that the languages are the same between the programs. This error repeated for each of the three languages.
Added: I am using Paratext 9.3 and FLEx 9.1