I have noticed a pattern.
1) I click the mouse to wake up the system,
2) PC powers on but (I have dual monitors) both displays are black, 2nd monitor power light is amber.
3) If I press the PC power button after a couple of seconds the primary display will turn on or basically the log on screen appears. (On a side note, while the screen is black I have tried to hit keys on the keyboard and when the display returns it tells me the password entered is incorrect)
On a another note, when this doesn't happen, and the PC powers on quickly like it should, after I log on and get the desktop then Explorer freezes for anywhere from 2-5 minutes. After which there are no further delays.
My friend has suggested that it may be due to S1-S3 types of suspend and that Windows just doesn't like my hardware. I'll update this if I can figure it out, comments are welcome.