Cmyhero, I don’t know which system you are using, or what angle you are sharpening at. So rather than a lot of back and fort I will relate an issue that happened to me that sounds similar.
I was using the WE 120 with the standard vice trying to get a low angle on a knife. Like you one side seems to go fine but not the other. Turned out my stone was hitting the vice as the blade was too short and angle was too steep. So look for shiny spots on the vice or jack screw if you are using the std vice (has 2 screws you tighten) it would also be prudent to check the same even if you are using one of them more expensive systems.
If the above is N/A and you have not had the opportunity to watch this video https://www.youtube.com/watch?v=-RrvnZRVc-I grab your favorite beverage take a look. It demonstrated the different types of stroke you use with the WE, why and when to use them. It was very helpful to me as I developed my proficiency with the WE. Still no expert but very comfortable with the knives I sharpen regularly. Having A USB scope is worth very penny ($35) as you can see if you are reaching the apex of the bevel, yes the marker is gone to your naked eye but maybe it isn’t. A very bright light placed in front and above the knife as it sits in the vice is invaluable, if you have not apexes the bevel you will see shiny spot where the bevel is rounded or pushed over.
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