Hmm strange issue, But I figured it out.

CRITICAL:yum.cli:Config Error: Parsing file failed: File contains parsing errors: file:///etc/yum.conf
[line 3]: mysql* nsd* proftpd* pure-ftpd* ruby* spamassassin* syslinux*

[line 4]: squirrelmail*

The problem is that line 3 and 4 are new lines, instead of a continuation of line 2. Fix that and it works, I figure someoneone will have that issue, since I googled it and nothing came up.