As with many bills that trundle their way through Congress, there are a lot of 'fine print' things in bills that can cause all sorts of issues. Some things slip through unnoticed until someone runs into trouble with them. Others don't.
This bloggers gives a fairly reasonable explanation as to why many gun-rights supporters were against this bill.
http://www.armedcandy.net/2013/04/the-universal-background-checks-bill.html
Don't get me wrong - I have no problem with background checks to help keep guns out of the hands of people who should not have them (felons, the mentally ill, etc). But I don't think this bill was the way to fix the problem.

What is the point of rules that are not enforced?