Ok, troubleshooting time.
First your said that you have this problem since not long after you add the second drive.
-Try to turn on your computer without that drive.
a) I suspect a faulty PSU there. The amount of power require to power up the second HDD may be the cause of the problem. (removing a HDD doesn't mean reformat: you will still have your data)
b) Other possibility: boot sequence have been change cause of the second HDD. And depending on your BIOS setting, you may not be able to see the info on startup...
If the computer turn on without the drive, get into your BIOS and change the boot sequence to make the OS HDD first. then add the second HDD and see if it boot.
If that dont work,
1- Clear the CMOS (reset your BIOS)
2- Unplug everything, exept the monitor. add one component at a time, starting with the CPU. then the RAM and finally the HDD. (BOOT Beetween each addition)
Oh, other thing: Dont worry about the lights right now, they are just an indication, mine are not even plugued