Yes, it is. Running yEd with the cross-platform Look-and-Feel can avoid menu issues when using non-standard system-wide menu font colors.
To use the cross-platform Look-and-Feel for yEd (supported beginning with version 188.8.131.52), you can add the following command line parameter setting when starting yEd: -Dyed.laf=crossplatform
(resulting in an overall command like so: java -Dyed.laf=crossplatform -jar yed.jar
This can be done in a similar manner as described in an answer related to adjusting the yEd memory settings.