Sounds like the HDD could be dying to me.
I know it sounds stupid, but have you tried listening to the HDD directly when it does this, for the constant same clicking sound over and over again?
No clicking sound, the windows time always is wrong at bootup... Could that be connected? I always correct it, but it is wrong again next boot up... Linux if fine though...

My Seatools for Windows can't locate drive & gsmartcontrol fails to send command, but HDDscan gives result, again confused about that... anyway here are the results...
HDDScan S.M.A.R.T. Report
Model: WL400GSA1672
Firmware: 12.06H12
Serial: WOL240018242
LBA: 781422768
Report By: HDDScan for Windows version 3.3
Report Date: 5/22/2015 3:35:49 AM
Num Attribute Name Value Worst Raw(hex) Threshold
001 Raw Read Error Rate 200 200 0000000000-0000 051
003 Spin Up Time 227 219 0000000000-162B 021
004 Start/Stop Count 096 096 0000000000-129B 040
005 Reallocation Sector Count 200 200 0000000000-0000 140
007 Seek Error Rate 200 200 0000000000-0000 051
009 Power-On Hours Count 083 083 0000000000-3294 000
010 Spin Retry Count 100 100 0000000000-0000 051
011 Recalibration Retries 100 100 0000000000-0000 051
012 Device Power Cycle Count 096 096 0000000000-1294 000
194 HDA Temperature 125 091 27 C 000
196 Reallocation Event Count 200 200 0000000000-0000 000
197 Current Pending Errors Count 200 200 0000000000-0000 000
198 Uncorrectable Errors Count 200 200 0000000000-0000 000
199 UltraDMA CRC Errors 200 200 0000000000-00E1 000
200 Write Error Rate 200 200 0000000000-0000 051