I ran into something that sounds like what you describe. I wanted just a Vertical scroll because it was going to contain many many things eventually, but not a Horizontal scroll. I used a table layout panel; set the Panel's Vertical size so that the VScroll shows; set the width to accommodate what will go in there plus whatever margin or gutter your code will use.
Then, in the TableLayoutPanel
set the width of the scrolling panel's to absolute (I used 2 pixels more than the panel.width). If/when the user resizes, all the extra size gets distributed to everything else. Basically dont let the scrolling panel's width change. Might have to/want to set a minimum form size too.
The things I was adding were all the same width, if yours vary, you might have to set it to accommodate the widest.
Not sure if you are encountering the same thing, but sure sounds like it.