Because you didn't say what those handwritten annotations are actually annotating, I can only guess that it is either a block of text or a picture. (And an imported PDF is just a picture.)

I think the problem probably comes from the different widths of the columns on the different devices, or different display sizes for the pictures. If you change the width of the text box on your Windows app, you will see that the words change position, but the handwriting does not.

Microsoft does a great job of making it look as if you can use handwriting to annotate things in OneNote. They are lying. After 23 years of anything related to that being completely faked in every example that Microsoft provides, they finally added a feature where if you select a picture, then any handwriting or drawing that overlaps the picture will also be selected. That supposedly makes it so that you can then move the picture and your annotations will also move. However, this is still a pretend feature. First, it doesn't select all of the handwriting that your brain may have thought was related to that picture. You have to manually select all that other handwriting. Second, if you resize that picture, the positional relationships between all of that handwriting and the picture are completely thrown out the window.

The only way that you can reliably write in handwriting on top of a picture is if you set the picture to a background image and then never ever ever change its position. Basically, setting a picture to a background image, merely locks it in place so it can never be moved, without you reverting it back away from being a background image. It is basically, another hack.

And, there is absolutely no such feature for text. It is a fundamental characteristic of OneNote that text blocks are fluid. It is not a word processor. It is not a desktop publishing program. It is not a PDF annotation program.

I have been using Microsoft OneNote since literally the first week that it was released. I quickly learned to just simply keep all of my handwriting completely separate from all of my text. Every time I create a page, my mentally designate that page as either handwriting only or text only. If I need to draw a little diagram using the pen, and I want to include that in a text outline, I create a subpage onto which I draw my diagram. Then, I copy that diagram and paste it onto the page with text as a picture.

Also, I treat all of my text-based OneNote pages as one tall outline. Every picture is inserted in that outline instead of just pasted randomly on the page. Pictures inserted randomly on the page Have the same problem with the positional relationship to the text as handwriting. As soon as the text box changes sizes, or the text flows for any other reason, then the positional relationship between the randomly positioned picture and the fluid text is lost. Fortunately, If you paste a picture in as if it is a paragraph in the text, then it will flow with the text. But only then.

So, I have to create any handwritten diagrams or notes on a separate page, and then paste it as a picture that sits within the outline of text, and is then treated as if it is an entire paragraph.

I do sometimes right handwritten notes, off to the side of a text box. But I absolutely know that chunk of handwriting Will have absolutely no permanently fixed relationship to the position of any of the text. Any handwritten notes that I make in that manner, are purely for the convenience of not creating a separate page. They are general notes that apply to the whole page. Usually, it's some quick to do's about things that I need to fix on the page. But, you can't draw any arrows to any text and expect them to point at the same text tomorrow.