A new hotfix for ConfigMgr 2012 was recently released to fix applications issues in an OSD Task Sequence.

http://support2.microsoft.com/kb/3007095/en-us

Along side with a some new R2 variables all application issues seems to have gone away.

SMSTSMPListRequestTimeout=120000

SMSTSDownloadRetryCount=5

SMSTSDowloadRetryDelay=15

Thanks to Jörgen for this post and for clearing up the use of SMSTSMPListRequestTimeout.

SMSTSMPListRequestTimeout = Value in Milliseconds