Hi David,
When you say "doesn't work", is it the "tilt" angle of the blade (bevel) or length position (not matching the tip)?
Unfortunately putting a knife in the vice the same way each time is not foolproof, ideally it should be.
The left side of the vice clamp is firmly secured in a vertical position, the right side floats.
If you are sharpening a FFG knife, the right side clamp can follow the knifes side angle and result in "knife leaning" (to the left) and therefore an uneven bevel.
The advice from Wicked Edge is to clamp the knife vertically by eye, which means it clamps a point "somewhere" down from the top, then pack the gaps at the top with foam tape.
It's not always easy to repeat this the same again next time you sharpen.
I believe the WEPS will be complete when it can clamp a knife with both sides of the clamp following the knife faces.
Then rotate the clamped vice and knife to a true vertical position.
The other element is the depth the knife is located into the clamp.
They provide a two pronged depth stop, but the two default options don't always suit, some people raise the knife or angle forward or back from the default.
If you vary from this guide/stop, then it's hard to repeat the exact mounting position again next time.
Are you using an angle guage or just relying on the pre-determined angle dimples in the base rod?
These angles are really only an indicator, as they are only accurate if you are using a knife that protrudes 5/8" of an inch above the clamp and use the same thickness knife clamped the same way as when they were created by WE.
I guess until a better mouse trap is made, you rely on the marker and adopt a technique you can repeat.
edit - The top vice screw grips gently while the the lower screw spreads the jaws apart to act like a vice.
I also suggest you vary the role of each screw, but to repeat that again next time, I guess it can only come with experience, a bit hard to measure and record all these variables?

I take PC photos (.jpg), (although a mod on the WE site laughed at this idea) but I add in comments/arrows with software and name the file to suit.