Omnisphere 2 does not auto-convert on launch for security reasons. You must trigger the update:
Take an hour this weekend to audit your Omnisphere library. Convert those old bass patches, resurrect those vintage pads, and watch your production quality leap forward. The upgrade is waiting. Omnisphere Patch Data Needs To Be Upgraded To Version 2
To resolve this, you must sync your software, patches, and soundsources using the Spectrasonics Smart Update Spectrasonics Access the Splash Screen Omnisphere 2 does not auto-convert on launch for