So you're saying that it approximately tunes it 100% if you ask it to, but then upon doing a re-analysis, it finds fault with it's last processing not being exact.
I also find that if you do things like this the audio starts getting messed up sounding (mangled) after repeated processing and bouncing of the same audio. Some note to note glitches start to appear upon repeated processing and flattening/bouncing. So it would be best to export/re-import I'm guessing. Though that takes a longer time to do, especially with the kind of numbers of times I have to do this with so many live tracks. Plus I have lots of bleeding since the mics are all open since it's on stage and no direct boxes except for elec. bass and elec. guitar (2 out of 10 players of which some are doubling on various woodwinds)....
Cubase 7.5.2 Currently testing Cubase 8.0 with OSX.9.5
Sibelious 7 for Charts
MacPro 2.8 GHz 8 core, Mac G5 PPC 2.7 dual + MacBook Pro 17" 2.8 GHz dual mac/intel
OS X.9.5 (MacPro 12 gigs RAM dual monitors ATI Radeon HD 5770 1024 MB card)
OSX 9.5 (MacBook Pro)
OS X.5.8 (G5 PowerPC)
MOTU 424 PCI, M-Audio interfaces
Variety of DAW software, plugins, accessories
A little bit of old skool MIDI rack modules and keys
Recording Studio for Audio and Video
Professional since 1970's and using Cubase since it first came out.
Composer/Arranger/Producer of Music & Video