Pretty sure it's no different from how the vanilla enderdragon works in the End. The portal always spawns at a specific Y-level, at the X and Z coordinates of the dragon when it died. I don't remember what that Y coordinate is off the top of my head, but it should be the same as in the End and as the portal that ate your corporeal attractor setup. Rebuild your setup a ways above or below the portal, and you should be fine.
That is, at least, if you're on MC 1.7 or before; Mojang changed the enderdragon fight significantly in 1.8 or 1.9, so I don't know how it works with RFTools in those later versions.
Also, as an aside, with an RFTools syringe, a dimlet workbench, and some high-tier dimlet parts, you can create a Mob: Enderdragon dimlet. Install that in a dimension tab, and the resulting dimension will have 4-5 enderdragons flying around near (0, 0). They will respawn as you kill them, for no cost beyond what's required to run the dimension builder. Yes, you can use this to farm hearts for Draconic Evolution; yes, doing so could be a bit overpowered.