How do I highlight PDF text properly in the Preview application?
This seems to be a bug in Preview. There's a related thread about this topic in which many people say they are experiencing the same problem. I too have just tested it out and see the same results.

There are 2 workarounds I can think of. The 1st is to select all the annotations and set their color manually:


Open the annotations toolbar.
Press the right-most button which will show you a list of all the annotations.
Select all the annotations.
Choose a new color from the annotations toolbar.


The 2nd workaround is to use the Python script from the same thread previously mentioned.