This will definitely not work directly.
You could use LabVIEW 6.1 to save your VIs in LabVIEW 6.0, then unse LabVIEW 6 to save them in LabVIEW 5.1. Then open it in 5.1 and built it. It's probably not worth it and might hit snags especially if you use features that are not available in earlier versions.
I would contact NI, they might have a simple upgrade path for your application builder. Is it possible you actually have the 6.1 application builder, but simply cannot locate the CD?