Unfortunately it turns out that this is more complicated than we expected. You are correct about it being normalization-related. When packages are added to ProGet, essential identifying metadata like name and version get indexed in the database, and versions are supposed to be normalized when used this way. However, it looks like this normalization is not occurring for Conda packages.
We don't want to just do the obvious fix and start normalizing them, as that could lead to duplicate packages getting added and issues with replication. So, what we propose to do is extend our feed re-index operation to detect nonnormalized versions and fix, and then start normalizing versions consistently.
Long story short - it's not going in tomorrow's release, but we have a plan to get it fixed.