If I understand your phone correctly - it has only one wire/jack coming out of the back, but allows you to use two phone lines - When you had two analog lines hooked up before, you had two phones, correct?
Does L1 of the digital phone work when you plug it into the L2 jack?
The new phone you have is looking for line 2 on the alternate wires. The analog phones each look for the signal on the L1 wires.
Remove the extra box you have for line 2 and wire it into the outlet for line 1. Line 1 should already have the yellow and black wires hooked up. Hook up the red and green from the L2 box to the red and green in the L1 socket. (Red was probably wired to yellow and green to black in the L2 box?) Get rid of the L2 box. (yellow & black are L1, Green and Red are L2)