Short update regarding the issue in this post. I went to NBI Main at Taft the following day. Best experience. Air conditioned waiting area at the lobby outside the room, fast data capture, and they gave me a receipt to claim. I didn't have a hit but apparently everyone who gets clearance for a visa will have to go through extra record checking and I had to go back in three days. I also went back to Ever Commonwealth after two to get the other one, since I paid for it.
To conclude, I recommend getting the E-Clearance from NBI Main at Taft if you need an NBI Clearance for any reason. It's very fast and convenient. You skip the encoding and payment steps, go straight to biometrics data capture and your clearance gets released if you don't have any issues. Just remember that you might have to go back in two weeks if you choose to have it done at another center. Also, read all the instructions and follow them to the letter. You can apply and find everything you need at the NBI website. Good luck!