Today is the first time I have attempted to annotate PDFs and it has been a bust.
Some text in the PDF is overlayed with gray lines.
The text box is black and it does not accept input.
It may have something to do with the fact that the PDF is a webpage. But I don’t know why that might be an issue.
I am attaching a screenshot so you can see what I am talking about. (I do medical research with an emphasis on male health issues, which should explain the article content 
)
The grey lines are supposed to be there. They show where Link Annotations are located on the page.
We have identified an error with the Note Annotation are looking into it right now.
Sure you do. Nudge, nudge, wink, wink. Just kidding! 
What are “link annotations?”
And regarding my research: I just spent two days separating the wheat from the chaff winnowing almost 19,000 research articles (with the help of DEVONthink). I’ve been up to my eyeballs in all things hormonal! 
Link annotations are areas of the PDF page that contain clickable links. Most of them were put there by the author. They are on a layer on top of the image layer. You can edit some of them by clicking on them, but there’s not much reason to do that. Click the hand to see a display without the grey.
PDF annotation can be a bit of a pain. Have tried a few methods and applications. Here are some comments on the challenges.
Not all PDF annotation tools follow the standard method. Adobe Acrobat, DevonThink, Highlights, DocEar all seem to behave nicely and the annotations are usable across these apps.
Some notable exceptions are Mac’s Preview.app, Mendeley, which use a non-standard format, which is ok for internal annotations but messes things up when you view the PDF on one of the standard-abiding apps mentioned above.
While I am pleased that DThink does follow the standard, I’m afraid that I find it hard to use. As was recently mentioned elsewhere on this board, the Highlights 1.4 app does a much neater prettier job of this. You can use it within DThink.
I have the same problem. The annotation popup won’t accept text, and all options are grayed out or non-responsive except for the Color option. Screenshot attached.
It sounds like you’re working on this. Thanks.
JS
As BULLFROG noted, these is an issue with PDF annotations in the current release, which will be corrected in a future update.
Personally, I never use the text annotation notes provided in Adobe’s design of the PDF format. Why? They are not part of the PDF’s text layer, and are not searchable, which reduces their usefulness to me. They are only plain text, so cannot include formatted text, clickable links, images or tables. This annotation mode is limited to PDFs, but doesn’t work on the various other filetypes in my databases. Finally, I don’t want to vandalize my reference PDF documents with unsightly markups.
Instead, I use the Annotation template provided in DEVONthink to annotate documents. Select the document to be annotated, choose Data > New from Template > Annotation (or press the included keyboard shortcut). A rich text Annotation document will result that is linked both to or from the referenced document (of any filetype). Text entered into the Annotation note is searchable and can include formatted text, clickable links to other documents, images, tables and lists. This is much more versatile and powerful.
