As a programmer that has done lots of advanced stuff in OSX I have to point out to you that for "us" upgrading software and especially the OS is NOT a simple task like it is for end-users.
All of the upgrade software is designed around the assumption your an end-user, that does not have any advanced utilities or OS X hooking "helpers" or debuggers or compilers or tools.
For every OS upgrade since OSX first came out, I have tried the upgrade path. And each and every time that has failed, sometimes the problems are subtle - like your pink hightlights. But after a few weeks I give up and do:
- Fresh backup (TM's plus I use Carbon Copy Cloner to make a spare external drive into a bootable image of my computer - just in case)
- Re-partition hard disk
- Virgin intstall of new OSX.
- I install with a dummy user "admin"
- Do all the OS updates
- Then use Migration Assistant to recover my user ID and everything else.
If I detect the problem still exists, erase and try again, this time I drop migrtion of something to see if the problem is sitll there. After I figure out what module is "tainted" I import everything else and manually install what I'm missing that was part of the tainted module.
Last two upgrades, this took 8 hours and 12 hours. I usually do it on a weekend so it does not interfere with work.
As we "speak" I am downloading Mountain Lion to try the upgrade... Who knows, maybe it will work this time?
I have my twin backups ready to go just in case....
Have you opened the Console program and READ through the boot messages? You might get lucky and spot a boot up start message for whatever is causing this? Google the name of anyhthing you don recognize to find out what it is.