The evidence is definitely pointing at Dual Scan mode.
What's odd is the first profile I did was single scan and I got a crap profile. So I'm thinking there are multiple issues here. In my case, I think the first target had patches that were too small (smallest the product will allow) and the error checking in the current version just sucks eggs. I say that because in an older version, it refused to accept the measurements and I was done. In the newer version it was happy to take that data and build a crap profile. The larger patch size (9mm) target sucked today because maybe I'm running into the bug you report with dual scan.
In a nutshell, i1P is simply not reliable in terms of scanning with an i1Pro, yet I've had no current issues with an iSis. I'm sticking with ColorPort for the time being but hopefully once this metal profile is complete, I can put the i1Pro back on the shelf and stick with the iSis. I still have to do an optimization of the good profile made today. I sent the CGATs data i1P built to CP and will measure there, then move that measured data back to i1P to build ten new profile. Don't know if it will work, but it should.
I should point out that the bad dual scan profile built to day looked good in terms of the gamut map and the soft proof. My client reported it was way off (way too yellow). So at least with this process, one has to actually make a print to know if the profile is OK or not. The older original profile gamut shape looked awful and it produced an awful print.