I was just doing a test index on Beketov. I manually did the DeWrp bit in my command prompt and put the sqf in my ALiVE folder and then just disabled object categorization to skip all of it and it all indexed properly.

I am having the exact same issue.

DeWrp.exe and the dll files are in my path, my @ALiVE and map folders are in my Arma 3 folder. I did a command prompt test and everything worked fine. BattlEye is disabled and file patching is on.