In my workflow for aligning pointclouds, I have found a method that works for our purposes... it is pretty awkward, but it gets the job done.
Directly after Indexing the pointcloud, without making any modifications, I open the RCP in an AutoCAD base file containing the project grids and/or architectural features. Before moving the cloud at all in CAD, I go back to Recap and Resume Registration. Then I add in "dummy" control points. A minimum of 3, and I try to space them out at the far edges of my cloud. When first adding the CP's I make sure to title them uniquely (CP1, CP2, etc) and simply parrot back into the cloud, the location data shown for a control point. Example:
CP1
Recap coordinates
X 11.3000, Y 7.2000, Z 0.9000
User input coordinates
X 11.3000, Y 7.2000, Z 0.9000 (I'm just repeating back into Recap, what it tells me for the location)
I then place the center of a sphere in CAD at the same X,Y,Z locations; thus repeating the CP's created in Recap (also use different layers for the CP's so that way there is no confusion later). Once I have all the CP's I feel I need, I define the cloud and all the spheres as a Group, and proceed to rotate and align the cloud in CAD. Once I am happy that the R (rotation), X, Y, and Z are all set where I want them to be, I simply check on the sphere properties and update the CP data in Recap to show the newly aligned locations. Now when I reload the RCP file back into CAD at 0,0,0 it pops right to the spot I want it to be. This can be especially useful in multi-story projects as generally offsetting the Z's to stack floors in any meaningful way can be a nightmare.
Notes: 1) As I'm in America, I generally think in feet and inches, so I created an Excel file to do all the unit conversions in a more automated fashion. This also allows me to save the data at the very end to a Tab Delimited TXT file, which saves me a little bit of time in the end updating the CP data.
2) This whole process is well beyond what I would like to be doing for alignment, as it is very time consuming and has many opportunities available for human error - which is never a good thing. I have posts elsewhere on this forum discussing ways that this could be better, but until there is a better fix from Autodesk, I hope this can help someone out.