It should not since XaaS blueprints reside in vRA, but we don't know what you're calling and how. Regardless, sounds like you need to correct your vRO inventory problem.
When you say you see to vRA servers are you seeing on under the "vRealize Automation" section (CAFE server) of the inventory and one under the "vRealize Automation Infrastructure" section (IaaS) ? If so that is normal and expected. Can you provide a screen shot? Removing and re adding should have no effect so long as you get the plugins configured correctly. Any reason not to use the embedded vRO server that is part of the vRA appliance? Also, what version of vRA and vRO?