Red and Green are the old Tip and Ring. Black used to be ground and yellow was for the bell circuit. At least that's what they were about 40 years ago.
Currently, the Red/Green is used for one pair and the Yel/Bl pair would be for a second phone line.
The only reason to not follow the connecting block identifiers is if it is mis-wired at the Demarcation Box.
I really need to see what your installation looks like. Are you using a RJ-11 connector (little plug connector that goes into the phone outlet) or straight wire to a connector block.
If you are using one of the RJ connectors, then the pairing is arranged differently.
Pair #1 would be the center two pins ( pins 3 & 4). Pair 2 would be on pins #2 and #5. This used to be used for a second phone line.
Can you send us some pictures of what you have? You can attach a digital picture by using the "Go Advanced" below the box.