It sounds like you're not slanting your clapper box to the side. All shapers have a method of tilting the clapper box to the side. Its primary use is for making vertical cuts. With the clapper box straight up and down, the tool will not deflect away from the part properly. You want to make sure that you slant the top of the clapper box away from the surface you are cutting.
I also received email this month giving advice for slanting the clapper box on vertical cuts. That fellow said the direction of the slant is not obvious and he learned the technique from a 60 year old machinist where he worked. Here's the rub. If you put your tool in at an angle or have an offset tool holder you can usually get away without properly setting your clapper box. But don't try. Do it the right way and it will be safer and have a better-looking part when you are done.
Clapper boxes Photos by Kay Fisher
In the picture above you can see my 9” shaper on the left has an adjustment for the angle of the clapper box by fixed offset with a bolt. The picture on the right shows my 7” Rhodes shaper has a continuously variable adjustment with a slot. It is set up for a vertical cut now with an offset tool holder. The amount of offset isn't critical. Any angle over a few degrees is fine.
I should mention that you always take a vertical cut by advancing the vertical tool slide down not by cranking the table up. On most small shapers there is no automatic vertical feed so you do this by bumping the ball handle once on each cut. Usually about 1/8 to 1/4 of a turn. When I got my first shaper I took all my vertical cuts by cranking the table up. When I watched Rudy Kouhoupt's video I was shocked to see that I had been doing it wrong all along. I thought I was the only person in the world that didn't understand this but recently I found another.
However, there are some shapers that are designed to make the vertical cuts by raising the table. The Alba shaper (made in England) is designed this way and even has the ability to couple the automatic traverse to raise the table. With this design it would be accurate to make your vertical cuts this way and you would not have to set the vertical cutting angle with a dial indicator.
Keep sending email with questions and interesting shaper stories.
My email address is KayPatFisher@gmail.com.