Seems like Batman played with the diamond drill and/or the Batpack! Now, while showing as depleted (and depleting energy normally), the diamond drill never stops working. I just went back to my base after my second full inventory load without charging it back
In case it's relevant, after the Batpack's number it shows ":26" all the time and it never goes down, while the Diamond Drill shows ":25" after it's block ID (I knwo this thanks to NEI, which I use for the recipes). The chainsaw, while showing the same ":26", seems to be depleted. I also checked using an empty batbox that the diamond drill had no charge.
Finally, after trying to work with the Diamond Drill without the batpack, it kept working despite being uncharged.
Mods: NEI, Portalgun, RP2, BC3.1.1. Logistic Pipes, Teleporting Pipes, Railcraft, Steve's Minecarts, Wireless Redstone, Forestry.
Edit: after a game restart the problem seems to be fixed.