It appears as though yEd is very fussy about the contents of the clipboard. I was using the Bluefish editor (v2.2.5) to create HTML code for pretty labels. yEd will not allow me to paste the clipboard into a label. I can paste the code into a TextWrangler document, copy it and then paste it into a label.
While I was experimenting I noticed that yEd has multiple clipboards active at the same time. I copied a node object and it would not appear in the Finder clipboard. I copied text from another source and I could paste it into a label. Immediately after editing the label I used command-v to paste into the document area and the node object was pasted in.
This makes me think that Bluefish must add enough extra information to the text for yEd to decide that it shouldn't go into the text clipboard.