PDF is not a pixel-perfect export format. Especially with text, it depends on the PDF viewer application in which you open a PDF document how the text will be rendered. Moreover, yEd does not include its own text rendering engine, but leverages Java's built-in text rendering support. As a consequence, text rendering in yEd depends on the Java version and on the exact state of the operating system on which yEd is run. I.e. whenever you update your operating system, text rendering in yEd may change.
That said, there are two things you can try:
- Use a different font.
The differences between text rendering in your PDF viewer application and yEd might be more or less noticeable depending on the font you use.
- Change option "Text Rendering Policy" to "Vectorized Text".
This way text is not embedded as text in the generated PDF document, but as graphic instructions. Vectorized text usually means very little to no difference between your PDF viewer and yEd. However, it also means there is no "real text" in the PDF document anymore and thus you cannot select and copy any text in the PDF document.