Robert,
My AGP is 2.2.2. Just out of curiosity I pointed to the folder with the shapefiles that I reprojected in the batch mode. Those shapefiles were recognized. I'm starting to think the shapefiles coming out of R are missing something that model builder is looking for but the batch process doesn't need. The original R-based shape files have the following files: .dbf, .prj, .shp., .shp.xml, and .shx. The batch re-projected shapefiles (the ones model builder recognizes) have the following: .dbf, .prj, .shp, .sbx, .sbn, and .cpg.