It's a problem with the front panel connectors of the case, not the mobo. Sounds like they're not even connected to the mobo.
There is a jumper block on mobos that allows you to connect the front panel connector from the case.
Normally they come with jumpers that permit the rear connector to work, like this:
|-| (| is the connector and - is the jumper)
It basically has a send and return on the same set of pins, and the return line is connected to the rear sockets.
Some mobos (ASrock, eg) have a separate set of jumpers to determine whether you can use one or both connections - most mobos don't and the same jumper block serves as an output and return.
First the jumper is removed, which disconnects the send from the return. They have to be physically connected to each other for the rear output to work. Some cases (as per the Intel FP audio spec) have switched connectors, so the front output when used will disconnect the rear output.
Some don't follow the spec and in those cases the leadout wires that connect to the mobo will have only one wire per channel, and two connectors on the same wire. When connected to the mobo, this is a dead short and now both the front and rear can be used.
Then there's HD audio, which requires a separate front panel configuration, and a compatible mobo, and then you can flexibly route audio signals wherever you want.