First, do not try to copy or rename the .idx files. They are generated on each run if not found. Basically what they are is a list of topics for dcts or verses for cmts. It is much quicker for the app to search the small .idx file than the large .cmt file. However, between versions of a module, the name will be the same but the data can be different thus every thing can get out of sync.
The best thing to do when in doubt is delete all the .idx files found anywhere under the Modules folder and then run Bible Analyzer. It will make new ones.
Second, the portable versions will only look for modules under the Modules folder in the same folder as the app. But there is a difference between 3.9 and 4.0. In 3.9 the modules must be in their respective sub-folders. Dct in Modules/Dictionary; cmt in Modules/Commentary; etc. But with 4.0 they can be anywhere under the Modules folder. Thus if one has two copies of a module say one in Modules/ and the other in Modules/Dictionary/, there will be two instances in the application.
Hopefully, this will not be an issue to the normal user, but I can see how it can be to beta-testers who are copying files and such to test.
The normal installation (non-portable) of version 4 will look for modules in three places. First in a new Bible Analyzer User Modules folder under the user's Documents folder; in the normal ProgramData folder and in the application Modules/ folder. I hope this doesn't cause problems. The issue is many users can not even find their ProgramData (All Users in XP) folder to work with their modules (they are hidden by default) so I made a user folder under Documents. This is where all user created modules will go. The official mods will install in the normal ProgramData folder. Things were simpler in the "old days" of Win-98. Now Windows complains if certain files are not in certain places.
Delete you .idx files and try again. Also, be sure the portable.ini file is still in the v4 app folder.
Developer, Bible Analyzer
But to him that worketh not, but believeth on him that justifieth the ungodly, his faith is counted for righteousness. (Rom 4:5 AV)