Have to reset BIOS to Default every time I switch out a drive?

During my long debacle with trying to set up RAID 1 on my new Dell XPS 8700, Intel 8 Series C220 - Z87, I ran into this problem and want to know if it is a faulty motherboard or is it typical: 

Last week Windows stopped seeing some of the new HDs that I installed. BIOS was able to see them. SATA Ports that affected were 2, 3, 4. Ports 0 and 1 were working. Dell tech came home, replaced the motherboard and all ports were working again. But now I added three more hard drives again, to Ports 2, 3, 4 and Ports 1, 2, and 3 stopped working again. The only ones working were Ports 0 and 4. Dell will replace the motherboard again. This is all in AHCI, I did not change it back to RAID during this debacle. 

Last night I noticed that if I go into BIOS and and Reset to Default BIOS settings, the SATA ports came back alive and all my HDs are visible again. Is this typical? My concern is, I will set up RAID 1 soon and I should be ok, until if a HD fails and I need to remove it from the array and put a new one back in. At that time, I may have the same problem again where the HD becomes invisible and I need to reset BIOS to Default, which will most likely wipe out the RAID due to defaulting to AHCI. 

Has anyone had this issue before? How do I work around this?

 Thank you.