Perhaps you didn't have an issue because you were stamped in N. Ireland and not Ireland as N.I. is still the UK. Where if you went through Dublin, then you'd have an issue as you wouldn't have a stamp from the UK on your visa.
It was actually in Dublin, Republic of Ireland that I've always been stamped. I don't have a stamp from Northern Ireland, or anywhere else in the UK on my passport.
When I moved over to Belfast from St. Louis, I went through Dublin, and the 3 times I've visited since I've done the same, and when I go through customs(which usually takes ages!) I finally get up to the Immigration Officer who asks, "
What's your purpose of visit?", and I always say something like, "
I Live in Belfast," then they flipped to at first my Visa, and last time ILR, and stamped it, but then wrote in with a pen "IT N. Ireland." (and after waiting ages to get to the guy, that process takes a mere 15 seconds!)
I think when I first got my National Insurance number, the lady asked me why my passport wasn't stamped, but I didn't have any problems getting my ILR.