It doesn't seem like there are any recipes for Rubyte or Bobmonium extraction with current version (used FNEI to look up recipes). My old maps have both raw ores lying around -- but now I can't seem to get either at all.

You have to do research to improve extractions/get new levels of extractions.
By researching "Electric Omnitractor 1" (still only red science) you get access to an impure extraction that gives you bobmonium and rubyte, be aware that this recipe requires an Omnitractor 1 or higher, that wont show up in a burner Omnitractor for example.

I figured out the problem.

There is an unlisted dependency for the current version Omnimatter, which was causing the Omni Sea Block Compatibility to malfunction (my Rubyte/Bobmonium omnitraction recipe-level was producing Jivolite/Sulphur). Enabling Flare Stack and Bobs Ores now re-allows the recipes for Rubyte/Bobmonium (since Omnimatter works again).

yep, once you play with Angels omnimatter requires BobOres to work correctly, even without SeaBlock.
Thats the reason why its just declared as "optional dependency", when you use Omnimatter without angels for example, you wont need Boores aswell.
I might declare BoBores as dependency for OmniSea to avoid more confusion