I have fixed the issue in fastqc_0.11.2+dfsg-2 Configuration directory isd now in /etc/fastqc to allow modifications and code has been patched to load files in this directory.
-- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
