Some clients do not get software deployment, actions missing after OSD

We have Win7 SP1 x64 rollout going on from XP, a refresh scanario on ConfMgr 2012 SP1 non-CU site server. Our testing phase went fine with 100% success, but just before starting rolling, I approved updates November 2013 - January 2014 and did too
quick test. So there was lot of issues, after that I had to disable those patches during OSD and let them be deployed via Software Center, after OSD.
Still, about 10% clients comes out with missing actions in ConfMgr client, or/and do not get desktop deployment software. We have 2 additional apps comming up to to user profile, so after first logon these 2 apps gets installed. And in 10% this does not
happend.
- bounderies are fine, client location .log is clear.
- usually ccmsetup /install -> reboot -> ccmsetup install with MP paraments solves the problem, but not always. It´s also too slow solution
- I noticed, that in this enviroment, the 3rd scheduled task called "Configuration Manager Maintenance" is missing. I only see Idle and health eval. I had similar case in my lab with R2, and that maintanced task fixed my client with missing in
10 minutes!
- our guys who installs Computers, claim that this behavior is seen more with refresh TS rather than with PXE boot - new machine scannario.
- there are additional role based applications with required deployments, and they do not appear, even if the actions are fixed
Any hints what to do? I would like to avoid upgrading site server to R2 or updating it during active rollout.

Skywalker - I agree, solving Software Updates issues in OSD is a challenge. It´s shooting ducks to figure what KB fix breakes the OSD hook. Recapturing .wim in a middle of a rollout is not the option here, but you´re right. In other side,
if patches breakes OSD during deployment and install software update step, it´s no guarantee the capture will solve your problems. I will check the registery, didn´t know that before. I have my suspesious, that TS might not finnish properly, though there is
no errors. MDT brings lot of more logs and status messages, so solving this isn´t easy.
Torsten - sometimes, waiting for hours, rebooting, killing and restarting prosess isn´t enough. Even if all actions are precent. Also, in a real life users can´t wait for hours. I´m very keen do understand, why there is no 3rd schduled task
of maintance.

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