I had the exact same issues. It took a lot of searching, but I discovered that I needed the "output-features" and "export-protocol" commands in my flow exporter.
- "output-features" - requires 12.4(20). Is required to send Netflow packets over the VPN tunnel
- "export-protocol" - requires 12.4(22). Specifies what version of Netflow protocol to export (v5 or v9).
Hope this helps!