.. sounds like you had a 40Gb drive that for whatever reason wasn;t operating correctly - it could be that this drive is damaged / faulty etc - you say you took it out and used another drive until you fixed it - what did you do to fix it ?
If the smaller 3.24 Gb drive worked on it's own then there may well be a fault on the 40 Gb drive that is preventing your PC from starting up when it is installed, HOWEVER make sure you have the jumpers on the two drives set correctly -
You should find these on the back of the drive where a small plug fits over one of a pair of small pins - depending where the plug is positioned on the pins determines whether the drive acts as a Master or Slave - there should be a label on the case of the drive to show the different settings ( if not search the manufacturers Web Site ).
The drive being used to Boot up from should be set to Master and the other one set to Slave.
Post details of what you did to fix the 40Gb drive.