I should be able to provide some assistance here. I used to work for a company that manufactured these orings for Chrysler, in doing so I(we) designed and manufactured the orings in your Jeep motor.
To conclude, you should use the new brown ones.
When the motor was originally manufactured, polymer manufacturers such as Dupont and Ausimont, produced only a certain variety of polymers that oring manufacturers could use to manufacture rubber. Well, rubber compounds are designed for a specific application. The orings used on the fuel injectors of a Jeep motor....any motor for that matter, have to deal with several things. On the intake side of the injector(the lower side), the oring will see more heat due to the temperature of the head and will not see direct fuel exposure. As such, that oring material must have better compression set(the resistance to becoming flat over an extended period of time) at higher temperatures, yet still be able to seal at temperatures as low as -20 F. On the fuel rail side of the injector(the upper side), the oring will see less heat, but will be directly exposed to pressurized fuel. Believe it or not, rubber is permeable, and the exposure to the fuel will cause the oring to swell. Therefore, at the time the engine was manufactured, polymer manufacturers did not have a cost effective polymer that oring manufacturers could use on both ends of the injector.
However, in the mid 90's Dupont(as well as other polymer manufacturers) started producing Viton(Dupont tradename) B polymers which could be used in oring materials at both ends of the injector in a cost effective manner that also satisfied the design requirements.
This only lasted a while though, OEM's started requiring that all suppliers produce systems that would seal to temperatures as low as -40F. Believe it or not, Ford/GM/ Chrysler beginning around 1998 would enclose a first run vehicle in an environmental chamber at -40 F for 24 hours, and then they would crank it, and it better not leak, or for that matter, vibrate loose. This resulted in the development and manufacture of the Dupont GLT polymer, which is typically an ocean blue color. Therefore, as folks start replacing the seals in Jeep 4.0 motors in 1998 and later, they should see a brown oring on the bottom, and a blue one on top. By the way -40F is really cold.