The startup sequence is a bit funky (and not entire predictable when it comes to timing, imo), but your's sounds a bit wrong. Here's my Wiwynn on a good run:
- Flip switch
- PSU fan revs up, light turns green, fan slows down to normal speed and light turns yellow. This means "Running, good". Weird, using yellow as "good", i know.
- Lower LED next to the hard drives lights up Yellow, also means "good". I haven't seen the top LED light up yet. If you trace the wires, they both go back to the power distribution boards at the front of each motherboard. I suspect the top LED lights when something is wrong with either the fans or the distribution board
- Node A fan revs up, blue led on board turns on.
- Node A flickers BPLED yellow (the outer-most led). I believe this is the "boot" LED
- Node A flashes HDLED yellow (the center led) a few times, along with activity on the drive. This is the HDD led
- 30-60s later, Node B's fan revs up, blue light turns on, follows steps 4-6
- When everything is running you should see:
- Yellow on PSU
- Yellow by HDD
- Blue on both boards
- Flickering yellow on center led from each board, indicating HDD activity
If a board powers up (e.g. fan runs) and has steady blue, but never flickers the center yellow HDLED, it means something is wrong. I've encountered it twice now: once when I was installing RAM (a stick was bad) and literally just now while checking, because it appears one of my HDD's just died (yay Seagate). After swapping the HDD the boot sequence resumed as normal.
It sometimes takes longer for the second node to power on. I suspect it relates to the last state the board was in. You can hold down the red button to cycle power. The grey is a reset I believe. Although both buttons seem more like "suggestions" than anything else, sometimes the board appears to just ignore them.
So... your board sounds unusual. I'd unplug one of the nodes, remove the graphics card and boot, watching for HD activity on the center LED. You could also try swapping the HDDs, and make sure the fans at the front are fully seated. Perhaps also try the second SATA port and power, just in case it's related to that. Is the coin battery fully seated? Are you sure the PSU is plugged into the 240v socket and not the 120 on the transformer?
Otherwise, I'm outta ideas