I am trying to scale two polys together to bring the edges closer in, I've tried all the action centers and setting the workplane to selection and again using all the action centers, nothing has worked so far. I would really appreciate some help with this one! The bottom image is usually the deformation I end up with, and the top is how the polys look originally.
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Try scaling the vertices, you might get a different result, failing that reset preferences maybe?
Not certain why it's not working with local scrub centre on just the polygon...
you might have a polygon with no parallel edges so whatever you do either one of corners tend to skew visibly because of oblong shape. in that case I'd just use slide tool to bring the edges closer one by one.
This happens all the time in Modo, the scale at which you work is not compatible with smaller pieces vs larger chunks on the same mesh. I frequently have to go in Preferences --> Input --> Units and change the increments.
I sometime have to compensate with manually changing the values while working ...