I am having an odd problem with my SCCM 2012 OSD tasks. It appears that not all applications are showing up in the "install applications" task. For instance, I have separate applications for 32-bit and 64-bit Java. The 64-bit application shows up in the list of applications you can choose to install, but the 32-bit version doesn't. I have tried both with and both without the "allow this application to be installed from the install application task sequence action without being deployed" box selected. (It also looks like that box does nothing, I have it unchecked for Acrobat Pro and it still shows up in the list).
Both deployments are working outside of the OSD stuff, but I'd like to be able to have them install as part of an OS deployment. Any ideas?