I have run into that as well over the years. The funny part about it, ok the sad part about it, is that many secular universities/colleges will not honor degrees/credits from ATS accredited schools (that don't also hold RA). Secular universities usually want RA for purposes of employment and many times for the purpose of further education. The school I am finishing my MA/History degree at holds this policy. I was talking with the chair of the history department a few months ago and he was telling me about students coming from Bible Colleges/Seminaries who wanted to get a MA/History, an MAT in Social Studies, or just licensure. The problem, however, is that many of the Bible Colleges/Seminaries these students are coming from either are not accredited at all or are accredited by agencies that are not regional. He, the chair, said he felt bad about turning them away but that he had to do it all the time. He even told me about a lady who has been forced to start from scratch because she earned a BA from a unaccredited religious school and needed an accredited degree to enter into the graduate program. The Univeristy did accept my MA from Liberty, as the North Carolina Community College system has, but only because it is RA.
So what I say is that if you might want to further your education at a secular school (teaching licensure, another degree, etc) you need to get your degrees from RA schools only. The same is true for those who wish to teach.
ATS and TRACS only schools are fine for ministers but they are not fine for students seeking an academic career. Those folks need RA degrees.