Issue: When deploying applications in an Image deployment Task Sequence in SCCM 2012R2 CU4,

ConfigMgr looks at the old revisions of applications when deploying and consequently fails a deployment.

This issue should have been resolved post release of SCCM 2012 SP1, however i have found it is still being experienced at SCCM 2012 R2 CU4.

This may be resolved by an upgrade to SCCM 2012 R2 SP1 since the documentation for 2012 R2 SP1 talks about it however, this is not certain

Application Management
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When you revise an application, the new revision now inherits all dependencies from the previous revision.
Reference:
What’s New in System Center 2012 R2 Configuration Manager SP1
https://technet.microsoft.com/library/mt131422.aspx#BKMK_OSD

2 workarounds in place that are known to fix the issue:

Workaround is to delete all the older revisions of an application.
OR
Disable the install software in the existing task sequence, save it and re-enable it.