I have the same board and as I know the republic of gamers logo is supposed to remain solid
The heartbeat effect is only when the board is asleep/hibernation or if it lost power for seeming no reason such as house lost power
The setting in the bios labeled pulse effect is for the republic of gamers logo in the bios itself that has the pulse glow go from left to right while your in the bios
At least that's what I believe as my logo has never pulsed unless my house lost power or my PC was in sleep mode
The manual even lists under the ROG Effects section that rog pulse is for the Rog logo animation in the bios itself
Onboard led controls the start,reset and motherboard rog logo
Then supreme fx lighting which this version of the board doesn't have since it has armor
CoolerMaster HAF 932 Advanced/ Maximus VI Formula/ I7-4770K/Swiftech H320/ Corsair HX850/ G.Skill Trident X (2x8) 16gb 2400MHz/ 2x 840 EVO 120gb(Raid 0)/ WD 1TB HDD (Backup/Storage)/ EVGA GTX 1gb 560 TI/ Asus 12x bluray combo