I will try to sum up the story as quickly as possible so people actually read this. My laptop works great and has since it was bought. A while ago for a reason I forget my OS got corrupted or something. I couldn't just fix it with a usb boot drive. It only allowed me to format everything without saving personal files. I did this, but prior to executing I turned off the laptop and removed the HDD to avoid losing my school data and etc. Windows did its thing and once it was done it booted like normal. I inserted the HDD again and ever since it takes about 100+ seconds compared to the original 6 or so. I have run bios diagnostics and came back with no errors on 2 full scans. I did a side by side comparison of the boot between the laptop with and without the HDD plugged in the same day as this was posted. Take a look for yourself, but I really dont know what is wrong.
One last thing. My bios does not show its settings properly. Under boot settings I only see windows boot manager, and in things such as the the F12 menu I find there is only intel rapid storage and UEFI something or another. My bios is not showing things correctly needless to say. Also safe boot and fast boot are on. I have tried to manipulate these settings and still no change if that helps. This computer is also half a year old.