Boot time slow after installing HDD

I have my OS and all applications on my 240GB SSD and I used to ave some games on there as well but It wasn't enough space so I bought a 1TB 7,200 RPM HDD and put it in the secondary HDD slot so all my games are on the HDD and everything else on the SSD and for some reason the boot time has slowed and the application icons on the desktop are white before they have the proper icon if you know what I mean. I looked on google and made sure the SSD was first priority and was on AHCI in the BIOS I even disabled indexing and turned off pagefile because I have 16GB RAM any other ideas? TY