I recently replaced the motherboard in my Dell Latitude E6410, and when I put it on my docking station; my docking station wasn't charging the battery nor was it being detected in the BIOS or Windows. However, I press the power button on my docking station (Dell E-Port Plus II) my laptop will turn on.
The previous motherboard I had in my laptop didn't have the nVidia NV3100m graphics chip on it, so it was using the Intel HD Graphics, which the CPU on that was an Intel Core i7 620M. Along side replacing my motherboard (that has the Nvidia NV3100M GPU), I put in a i7 720QM along side. I do have a 130 Watt adapter on my docking station for those wondering.
I have looked in the BIOS/UEFI and haven't been able to find any options dealing with the docking station and have also updated the BIOS to version A17; no luck on that.
Make note, when I had the 720QM on the motherboard I had in my laptop prior to replacing did work with my docking station, since the LED lights lit up.
It's entirely possible for the dock LED to light and for the Power button to work and for your system's underside docking connector to still have a problem that prevents it from charging. In your BIOS setup under the "Battery Information" section, underneath the battery icon you should see a field called "AC Adapter". That will show you the wattage of the detected AC adapter, regardless of whether it's connected directly or via a docking station. Does it show "Unknown" or "Not Connected" when you're docked? If so, then if you haven't already, try undocking and then connecting the dock's AC adapter directly to your system just to make sure the AC adapter's wattage is properly identified in that configuration. If so, the problem is either the dock itself (do you have another one to test with?), or else a problem with the new motherboard.
I have confirmed that the BIOS said no charger is even installed while I have the laptop docked, and sad to say, I don't have another docking station to test with.
Edit: Just for giggles, I slapped my battery slice on and my motherboard picked that up within a couple of seconds. So I know my docking port still works. So it might be my docking station.