There can be a difference in .223 and 5.56mm factory ammunition at least when fired in some rifles. This quote is from the Bushmaster Q&A section:

"The NATO Spec 5.56mm chambers have a longer "leade" or throat than the SAAMI Spec .223 caliber chambers which have about half of the leade or throat of the 5.56mm chambering. While it is safe to fire both 5.56mm and .223 caliber ammunition in our rifles, the 5.56mm ammunition should not be fired in rifles chambered in .223 caliber as they will develop very high pressures."

http://www.bushmaster.com/faqs/afmmain.aspx?topicid=&faqid=&question=

Like you I have fired handloads using 5.56mm military cases in AR type rifles with no problem.