Are you running the most current version of i1profiler? This problem was very common with the 1st release of the
software (at least on the windows side). For about 3 months, I had to use a modified version of the code that changed the color lookup table. Net my 9880 was printing too dark for the software and I would get the same error constantly. You could fix the problem by backing off the ink density about -10, but I didn't want to do that as a permanent fix.
With the 1.1.x update of the software, this problem went away.
When I was having the problem, most times if I did the individual scans of the problem colors, when I generated the profile, it didn't look right on the 3D view, i.e. it had big holes in it. By backing off the ink density, I got good profiles.
With the fix from xRite, this problem went away and has stayed fixed with later versions of the software, Win7, 64 bit.
Paul