http://bugs.winehq.org/show_bug.cgi?id=51345
--- Comment #21 from Hans Leidekker hans@meelstraat.net --- (In reply to Hans Leidekker from comment #20)
Looks like the missing assemblies are v1.0 assemblies while the ones that are installed are v2.0.
This is because builtin fusion is no longer used. wine-mono installs a copy of fusion.dll for each major .NET version while native .NET 2.0 installs only one, which does support installing older assemblies.