I'm hoping this will help someone on the forums...
I was having this exact same problem. Packages would install fine during my OSD task sequence, but Applications failed. Looking through logs, I saw various errors: 24(Application download failed), error code 0x87D00607, etc.
I tried everything I could think of, updated content on distribution points, deleted and re-created applications, etc. Even confirmed I had boundary groups set up correctly.
Finally, it dawned on me that I had recently set up the migration piece between our old SCCM 2007 hierarchy and had enabled distribution point sharing. This step created boundary groups so SCCM 2012 clients could connect to SCCM 2007 DPs. In these new groups, there was one that contained AD sites that were in my new SCCM 2012 boundary groups. This created duplicate boundaries and my clients didn't know where to go for their content. Once I deleted the boundary group created from sharing DPs, applications installed correctly.