I have tried, unsuccessfully, to recreate the problem you described. Using yEd 3.17.2, and the "Entity with Attributes" node, the PDF output text of all labels can be selected and searched in the following cases:
•Node added directly from palette with default text
•Node with a label added to the top compartment
•Node with another node converted to a label in the top compartment
•Node with an additional top label and bottom label font changed
Can the label text be selected and searched in a PDF if you use the default node labels? If that works, then there may be other settings that are causing the behaviour you observed.