Yep I have found that two piece quivers don't "play nice" with hard cases. I like two piece quivers and thankfully I also prefer soft cases.....a match made in heaven.
If you like the case more than the quiver, get a one piece that you can take off of your bow when you store it. If you like the two piece, get a soft case and leave it on. There are many soft cases out there. Mine has an arrow pouch with a hard case arrow box in it. It even has an inside pocket for my tackle box and yet another inside pocket for misc. stuff like my release, gloves, mask, tags, flashlight, grunts, pad and pencil, etc... It is large enough that I can store my bow with arrows in the quiver.
I will see if I can post a pic. of it.
Edit: Pic
You can see the external arrow pouch, it has a hard case arrow box inside.