Update: Some readers of my blog still experience this issue, and up until now the exact cause is not clear. The workaround is still valid though ! Please read the comments below for the latest updates. If you also experience this issue, please up the counter on the Microsoft Connect site where this issue is reported: https://connect.microsoft.com/ConfigurationManagervnext/feedback/details/772079/task-sequence-doesnt-install-or-fails-when-application-version-is-updated
Recently I experienced some strange issues with installing applications during a task sequence, and at this time of writing there is no official fix for this issue in ConfigMgr 2012 only a workaround. It caused me a lot of question marks before i could actually figure out what the problem was.
So, to start let first answer the question about what the symptoms are:
When you install applications you will notice that the task sequence when executed will not install the latest application revision of that application. Instead the application revision of the Application at the time it was added to the task sequence is used, causing either the Task Sequence to fail or an earlier version of the Application ends up being installed.
When looking to the References of your task sequence you will notice that it displays a reference to the latest application revision you have.
This corresponds to the actual revision, which you can view by right clicking on the application and by choosing Revision History. As you can see here Revision 2 corresponds to the /2 behind the Application ID.