Welcome to the Wicked Edge Forum Brandon…from the description of your issue it suggests you are using a WE100, WE120 or We130 system with independent angle adjustment on each side. As Mikedoh stated the angle degree markings on the square bar are there just as a guide to help get you in the ball park with your adjustments and are not intended to be used as an actually measuring device.
There are many early and more current Forum posts written on how to deal with the issue you experience. I invite you to read and search the Forum for these answers. Here is an earlier Forum Post for the similar situation experienced by another Forum Member. Please read the post follow the blue links, this should help. The clamping system your using can clamp the broadest variety and width knives of any of the WE systems. Along with that the learning curve to utilizing that clamping system is larger and requires more manual interaction on your part and more time and experience to gain confidence with it.
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