Weird light issue. Need help please

This a truck built somewhere between the mid 2000s and now? Could be the new lights are drawing such low current that the body controller doesn't recognize there are lights connected.

Another possibility is what voltage are the lights?

 

Check current and voltage at the connection, may be too low and your new lights dont like it

Pita but could just run a new circuit there...

 

Also, check that there is not excess dialectric gell on the connections. I have installed new led lights and have had to clean the connections to get them to work.

 

What were you using to test the polarity of the plug in the truck? Multimeter or test light?

 

Most low output LED lights have a bridge rectifier on the input which will convert AC to DC and no matter which way the power is connected it will route the polarity to the correct input.
I would check the voltage at the lights that are not working with them all connected to the circuit. With multiple lights in the circuit there will be splices in the harness and one may be failing due to corrosion. The new lights may be drawing slightly more power than the old lights causing a larger voltage drop. The light that had some LED's out was probably the last light on the harness.