I cannot help, as I have never worked a planer blade, so I'll just be following this one. I have the planer blade jig, but my planer uses "disposable" blades which are too narrow to sharpen. I didn't realize this when I bought the jig. Disappointed.
Have you checked flatness of the jig surfaces themselves? Seems crazy as these are extruded pieces, but maybe...
I checked the plastic strip on my jig. It also has some small bumps and is not completely flat and smooth. Not sure of the sizes available, but I think Tormek sells a "sliding surface" adhesive backed plastic material. If they don't offer something long enough, I'm sure something is out there. I know I bought some for the scissors jig. I have some in tape form but I cannot find my roll right now. Here is a source of different types of tape:
McMaster-Carr.
Another thought is that the USB bar can flex a bit towards the unsupported end. Not sure if that would result in the type of non-flat edge you are experiencing. From looking at the Tormek video, I think it should be possible to rig some sort of support for the free end.
Like said above, I'll be following this. But there are not many users of these jigs, so I'm not sure how much help there will be. Probably best if you contact Tormek support:
support@tormek.seRick