It is very likely that your BIOS is not set correctly on one item. In BIOS Setup there is always a place where you can specify what device(s) are to be used to boot up. If you have more than one possible, you can set up a priority. For example, I have mine set to try my old floppy disk unit first, then one of my optical drives, then a particular hard disk. Under normal circumstances, the floppy and optical drives have nothing in them and, after a quick check, the system boots from the hard drive. But on rare occasions for troubleshooting I can put a bootable floppy or optical disk in and boot from that before it ever tries the hard drive. But that's just to illustrate that you can have a priority sequence. In your case, OP, you may only want to specify exactly which hard drive to use.
To do this you need to know how to enter BIOS Setup, how to move around in it and use its menus to make choices, and how to save those choices to be used all the time. So, post back here exactly what maker and model number of motherboard you have, and we can look up its manual and show you the details. Also, IF you have the manual yourself, let us know. Otherwise we could show you where to find one on-line to help you.
With that info we can tell you how to set the correct option in your machine so it always boots from the correct HDD.