I searched long and hard to find what was causing swfupload to fail on my cPanel, but work on my test environment so I thought I better save the result incase I need it again.
/etc/httpd/conf/js_modsecurity/useragents.conf. Simply remove the line below, or comment it out by putting a
# in front of it.
SecRule HTTP_User-Agent "^Shockwave Flash"
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