My guess is that probably when you modified the XML directly the issue was created due to line breaks or spaces. Either you accidentally created a space or line break without realizing, or your text editor uses a different line break format than what BatchPatch is anticipating, causing things to appear correct to you as the viewer, but in the actual data of the text file it’s coded differently (for example ‘\n’ vs ‘\r\n’).
I would suggest that instead of creating a brand new job queue from scratch, you simply use your existing job queue as a template for the new queue. So if you go into the job queue window and load your saved queue by double-clicking the saved queue in the list of saved queues (or by clicking the double-left-arrow), you can then give it a new title, and you can replace just the specific steps/lines that you care to replace. Then save it. This way the old queue will still be there, and now the new queue will also exist. This should be quicker than exporting to XML, modifying, importing. And it will also ensure that things work properly in the new queue.