I took it apart and investigated, and I found out that the threads were hitting two small bumps inside the screw guide (see pictures). These bumps only exited in one of the two guides, and totally rendered the tool unusable due to how it got in the way of the threads and stopped the screw from being seated correctly on the file.
To anyone who owns and uses this tool: Do you have this issue? Do you have two guide holes without and bumps impeding the screw tooth from sitting flush, or does one have bumps like mine? Is this a manufacturing defect?