Hi Chris. Premiere Pro normally expects folks to set up their sequence (timeline) in a standard deliverable aspect ratio.
I presume you selected an HD720p resolution (1280×720 progressive scan) sequence (timeline) whether or not you realized you did that. Because that is the format of the sequence, when you go to render ti will fill the unused space with black letterboxing (top and bottom) or windowboxing (sides).
To avoid this you must set your custom resolution wither when you create the timeline, or change the values when you render. For example, when you get ready to render, go to the video tab, unlink the horizontal and vertical resolution, and change them to the output you desire.

I pretty much always work in standard aspect ratios, so I don’t do what you are doing. If Premiere Pro refuses to accept your change in aspect ratio, you can always set up a 1280×1280 comp in After Effects and render your final deliverable from there. But I think Premiere Pro will let you do it without that step.
System:
Dell Precision T7600 (x2)
Win 7 64-bit
32GB RAM
Adobe CC 2015.02 (as of 6/2016)
256GB SSD system drive
4 internal media drives RAID 5
Typically cutting short form from HD MP4 and P2 MXF.