There's a solution, but it involves changing cable connections and maybe physically moving drive units, as sm625 has hinted.
You have two HDD's sharing one PATA port and cable on a mobo. Perfectly normal. However, the mobo BIOS is of such an old style that it only allows for booting from the Master device on that PATA port. Now, you know that the Slave HDD CAN boot, but only when it is the only HDD on the cable. So your solution is to swap drive units - that is, convert the current Slave unit to be the Master, and current Master to Slave. Then the one HDD that HAS a bootable OS on it will be the port Master device and it will work.
There are two (Maybe three) steps to do this.
1. Change the jumper settings on each HDD unit. In each case, use the jumper diagram on that unit - do not assume the diagram on one unit is the same as the settings for the second unit. Take the current one set as a Master and set it to be a Slave. Take the current Slave unit and set it to be the Master - or, if this is a different option, to be a Master with Slave Present.
2. You must re-connect the wide data cable ribbon differently. The END connector (usually Black) MUST go into the HDD that is now the Master, and the middle connector (usually Grey) must go to the Slave.
3. Getting those ribbon cables into the correct HDD units may be tricky, depending on cable lengths, etc. So you MIGHT have to remove the two HDD units physically and re-install them in the opposite slots, just to get Master and Slave units in convenient locations for cable attachment.