Neo2-FR won't power up after sitting for ~3+ standby - if less, it does power up

Hi all,
I had my Neo2-FR for about three months and have been working well going into standby (S3) and restarting by pressing the power button, until last week when I replaced the CPU fan with 120mm Scythe Kama PWM fan. I don't know why a fan would prevent the PC from Powering On, so I'm baffled. Even more bizarre, it works fine if when the PC goes into standby and brought back up in less than 3 hours or so (an estimated number). So, this mainly happens when I go to bed at night, I press the standby key on my keyboard and the PC goes into the S3 state. When I wake up the next morning, I press the power button to wake the PC and NOTHING - no boot, no power. I have to unplug the power cord and leave it out for few minutes and plug it back in and then everything works fine again. Here are the details. Please help!!!
My PC Spec.
Mobo: Neo2-FR (v1.2) BIOS Ver 1.85 (beta) - This hasn't changed. It was working fine before the PWM Fan.
Video: ATI HD2600XT 256MB DDR3
PS: Antec EA-500 (500w)
OS: XP Pro SP2 & Vista Ultimate (dual boot)
CPU: Q6600 B3 (333x9) 3.0Ghz - 1.325v (this is the same as before the Fan)
Heatsink: Tuniq Tower with 120mm fan with fan control (comes with the HS). I replaced the fan with above mentioned Scythe Kama PWN fan and the problem started.
Memory: Corsair CM2X2048-6400C5 (2GBx2). The setting is at SPD - 800Mhz, but voltage is set to 1.9v
HDD: 2x500GB Samsung 501LJ in RAID 0
DVD RW: NEC DVD-RW
Everything is exactly the same for HW, SW, and BIOS setting before and after the PWM fan install, except for the following.
1. Replaced the Tuniq's stock 120mm fan (3 pin header with rear mounted fan control) with Scythe Kama PWM Fan 120mm.
2. When the fan was replaced, I changed the following BIOS Setting:
a) H/W Monitor Menu: Enabled "CPU Smart Fan Target" and set it to 40C
b) Set the "CPU Min.FAN speed (%)" to "50%"
Only weird the that existed from the very beginning, but I never follow-up since the PC worked fine is the LED Status Indicator (LED3). The manual (on page 2-23) states the the LED3 "lights when system is on standby mode", but on my board, this light is always on. Doesn't matter if the PC is ON or STANDBY or OFF. As long as the power cable in plugged in, the light is on. Also, the light never changes color - it's always red. Is this normal?
This is really difficult to troubleshoot since I have to wait 5 hours or more to see if my changes fix the issue. So far, I've changed various setting in the BIOS, but nothing helps. To be honest, I'm not sure what to try.
Thanks in advance for the help everyone!
UPDATE: I've given up on BIOS setting and switched from fan header from the 4pin CPU to Sysfan5 (spins a full rpm with no fan control) and the PC boots fine. So, I guess by next step is buy another PWM fan to rule out the fan. If the 2nd PWM fan does the same thing, can I assume the motherboard is defective? Or is this a bug? Just to be sure, I'll leave the fan connected to Sysfan5 over night tonight.
UPDATE2: This morning, the PC booted just fine when the Kama PWM fan was connected to the a sysfan5.
If someone is using the stock CPU HS and Fan which uses 4pin PWM fan and they're able to use S3 (sleep and wake) properly, please post. If so, I can assume the motherboard is defective.

I made what I consider the dumbest of all mistakes in that I did not "correctly" follow instructions. I knew that I needed to unplug the unit to let it "reset", but I failed to completely disconnect all the components. The unit was obviously getting some trickle from the battery in the router that also controls my phone. The lesson here is that when you disconnect the power to let it reset, be sure that it is completely disconnected. Lesson Learned! Thanks for the help.

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