I suffered the same problems.
Solution: I realized that the version i was using (and automatically downloaded with
sudo apt-get install fastqc) was 0.11.4 (0.11.7 has been released this year).
I have installed 0.11.5 referenced here, and completed my analysis without issues. Worth to try :) (I use ubuntu 16.04)
I've had this problem as well - I'm not sure what the cause of it is. However, an easy work around is to first uninstall FastQC - "sudo apt-get remove fastqc" in Ubuntu. Next, find and go into the fastqc directory - you can open the application from here without installing it. Just type "./fastqc" and it'll open. I've never had issues running it this way.