To reproduce:
1) Create new rocket
2) Use tinker panel to add a second FuelTank modifier to the fuselage part with a fuel other than RP1/LOX. 3) The RP1/LOX tank no longer has a "tank set" and the validator warns that the engine has no fuel source. If you launch, the engine will not ignite.
Proposed solution:
The CreateFuelSourceForConnectedParts and FindConnectedTanks methods in the CraftFuelSources class should be rewritten to produce and use a lookup dictionary that is indexed on both part ID and fuel type instead of just part id.