Might be some mal-ware or a legitimate background task, so you might ctrl-alt-del and see what (all) is running in yer task list and apps list.
Is the MB the only diff?
everything else carried over and was fine?
You could ...
1) Plug drive into another sys as a secondary
(non-boot) drive ... to see if it continues the blinkity thang.
2) Check the drive status in setup, jus to see if all looks kosher.
3) I don't know if having "drive indexing" enabled might do that.
4) Run HDD diags
5) try a known good drive in place of "blinky"
These steps may not be "primary" or methodical or efficieant and, the list is certainly not complete but, just some stuff to try until a true guru chimes-in and explains what is really going on.
After a week on it, I found out it was not caused by the HDD but the DVD drive. The SATA controller is constantly polling for the DVD drive if the media has changed and flashing the LED about every 1 second.
I tried disabling the DVD drive and the constant flashing went away. :-)
I know this is not something to be really concerned about but I hope this will help anyone who may experience the behavior.
If it happenned to you, it will happen to others and, if you came here ... so will some of them.
I ALWAYS *very* much do appreciate hearing of the actual, final, proper solution. A small percentage of folks ever return to the forum to report. Too bad. sometimes it is because they felt stupid what was really wrong ... most of the time, they are just on to whatever is next.
I would even like to know what bios settings, or SATA connector, or firmware setting (or update), etc., will finally make the system behave as advertised, desired, and expected.
I, for one, will file this in my knowledge base and, hopefully, I will be able to "key" on it, when I observe similar symptoms.