Ah that mightve been it. I customized the Icon Template using the default one, making a layer, and overlaying my custom ones with the default then deleting the default layer, but I may have resized my custom ones incorrectly (it doesnt actually list anywhere what the individual icon size should be per Icon), so that may be causing the glitch. I'll try with the defaults.

Yep that was the issue. I also renamed my custom Icon file so that I would still have a backup of the original, instead of backing up the correctly way (I.E. Copying the original to a Backup folder then replacing the first one with my custom one having the same name). Thanks!