I know this thread is old, but I decided to answer this since I was able to fix the disappearing icons on my Thunderbolt build. I'm slightly off-topic here, as I am using a GA-Z87X-UD5 TH board which is Thunderbolt 1 rather than Thunderbolt 2.
My config:
Z87X-UD5 TH
Just Integrated 4600 graphics
Apple Thunderbolt Display 27"
I had to do the annoying Windows install first to have the link negotiation on the Thunderbolt side behave correctly, after which the Apple Thunderbolt Display would work correctly even during system POST. I did set the link negotiation to Legacy in the BIOS.
All the ports and whatnot on the ATD work correctly. The FaceTime camera, the USB and Firewire ports, and audio are all working fine.
I removed the kext for NHI, and like for everyone that fixed the slow boots. I did still have the disappearing / reappearing icons and clock on the menubar, which was maddening. I Googled a good bit and found many threads reporting the problem and none fixing it. It's worth noting that the icons disappearing isn't the whole problem--it's just a symptom. Those helper apps are actually not running, so for example when the Spotlight icon is missing you cannot use command-space to search for something--the applet that provides that shortcut is not running.
Checking the system log showed that com.apple.SystemUIServer.agent was segfaulting every time it started. Further was the data point cited by others that there is no dynamic TB device enumeration or access going on... OSX just sees the downstream devices as PCI devices connected via a bridge that it evidently decides is ExpressCard. Based on those nuggets, I decided to delete the ExpressCard (and actually two others I didn't care about) menu helper apps.
I did the following:
Code:
sudo su -
mkdir /tmp/moved_helpers/
cd "/System/Library/CoreServices/Menu Extras/"
cp -R ExpressCard.menu Ink.menu IrDA.menu /tmp/moved_helpers/
rm -Rf ExpressCard.menu Ink.menu IrDA.menu
What this did was delete those helpers from being loaded. Within ten seconds of doing the removal all the icons showed up and I have had correct behavior from everything on the menubar. I see the AirPlay icon and it shows a local AppleTV, etc. etc.
I suspect a lot of people are having this pain point if they are using a Thunderbolt Display because they are building a Hackintosh to replace a Mac Mini that Apple is evidently not ever going to update. I may cross-post this somewhere else in Post Installation in the hopes it'll be useful to others.
Cheers.