2012R2 Application installation steps after deploying OS from Task sequence is slow after applying hotfix 2910552

Question

We are currently using CM2012r2 for Endpoint protection, and in trying to save licensing costs, I have been given the task of doing imaging and application deployment through CM as well... everything started off well... noticed that imaging took a lot longer
than I remembered when I used CM2007 at my previous employer. Found we needed hotfix 2910522 and what took an hour to download now only takes 5 minutes (yay!) Then started other strange issues.  Mostly the fact that in the task sequence, the install application
blocks (we have 3 with 4-8 apps each) suddenly got really slow to execute. (boo!)  The application blocks eventually finish, but take about 5 hours and only the last block actually installs.    For example: 7zip takes 15 minutes to "install"
but since it isn't in the last block, it doesn't in fact install on the system.
so here is what I know so far:
Updated the boot image after applying the hotfix
Added the hotfix to the Windows and configmgr setup step command line to install the patch
Verified that all applications install correctly outside of the task sequence.
Created a new task sequence just in case the hotfix messed something up.
here is what I've noticed:
Only happens on workstations that have been imaged previously by CM (even if I remove the machine from AD and CM)
New machines image just dandy
not hardware specific (tested on 5 different laptop models and 3 desktop models)
workstations that have the issue, when finished, only installed the applications from the last block (4 apps) and none from the previous 2 blocks (16 applications)
If imaged new (not previously known) it installs the client correctly and it checks in, ones with the issue are in internet only mode and don't see the PKI cert for the machine, and will not check in.
Things I've checked, double checked, verified, and done:
All applications have the box for "allow this application to be installed from the Install Application task sequence action..."
applications are on all distribution points
Distribution points are healthy
One MP/DP was complaining about how it couldn't access a SMS folder.  uninstalled the roles, let it sit over the weekend, reinstalled this morning
Verified that the servers were on 10Gb full and were not throwing error on the line
Antivirus scanning was not scanning the store (used the built in template for scep)
Next steps that I am going to try:
create a new task sequence and split up install application blocks to only have single applications in them
recreate the boot wim for the media
 Thanks in advance

Answer 1

So this issue of yours is in B&C -task sequence? You're using capture CD for capturing, why? Why not automate the build entirely.
I'd suggest you add this:
http://support.microsoft.com/kb/2775511/en-us to your BUILD image (either online of offline, in the WinPE -phase), it fixes many WMI related problems.
After you've done your golden .wim, deploy it to your clients.
We don't do a build and capture because certain applications require handling on our part. Management has said it needs to be a certain way, therefore this is how we have to build it.  (mostly settings, and views that can't be controlled through registry,
Group Policy, etc.)  There are users that if they have to click on an accept button or it isn't the right color, or they want a different icon in their lab, then they go to the top and it comes back down to us, and our lives become miserable.
We create the image in audit mode, capture it using boot media, and sequence in things that are updated constantly (flash, shockwave, java, etc.) through the task sequence.
in relation to that KB, why would it work on new machines but not ones that have been touched before?