I noticed that the latest Proget version has a v3 connector for nuget so I added that and also re-indexed the package store, recomputed the checksums and deleted invalid packages. While running the re-indexing I encountered three errors that indicated bad packages (files in use), so I deleted all three packages, ran the re-indexing and everything appears to be working again. I suspect the problem was the bad packages in the store. Thank you @atripp for your help in this matter.