Just installed guts of PC into a new case which has a hotswap bay. I have a feeling Windows has somehow dropped AHCI drivers for standard MS IDE drivers at some time for all channels besides the channel the SSD is on causing HDDs to not be recognized until reboot when connected to the hotswap bay. -AHCI has been enabled to install Windows 7 on to SSD from the start so I know the SSD is using AHCI. -Hot swap is enabled in BIOS for port connected to hotswap bay. -Under device manager IDE ATA/ATAPI controllers all channels besides Channel 6 (SSD) say ATA Channel 1 through to 5. -Value says IDE channel for 1 through to 5. -I have installed intel chipset drivers I have a feeling channels 1 - 5 are supposed to have a description something along the lines of what Channel 6 reads. SOLVED:- Turns out I needed Intel Rapid Storage Technology software to enable hotswapping.