I am currently running Minecraft with the 1.7.2 update of Too Many Items installed. Playing on an AMPLIFIED world. Single player.
Opened survival inventory. Clicked on slot 7 in inventory. A vanilla diamond shovel was in the slot at the time. I clicked it to pick it up, and found a strange black bar coming from the affect I had with a beacon. Melded into the first slot of armor. Encasing arrows appeared as if the "Strength" icon didn't exist. Inventory doesn't matter.
Diamond beacon, max, strength. Vanilla shovel in 7th slot. Pick up the shovel, observe right corner.