It sounds like you might be using the default gearing strategy (stat weights) - which are based on a typical character, not specifically your character.
To run a custom setup, follow this guide: http://i.imgur.com/wBitmQb.jpg
The custom setup will sim every trinket and legendary and any item with a proc, along with the stat weights. Then it bundles the proc simulation data in with the stat weights so that procs get ranked from the sim data. This is important since stat weights can’t rank those.
If you run a custom setup (or need help, let me know), and it still isn’t working… link us the report to your custom stat weight simulation. Also post your text-string that you are using for best in bags and we can reproduce what you see and do some troubleshooting. But the custom stat weights will likely ‘fix’ what you are seeing 