I have found a reproducible boot freeze (on two boards); could someone else 
possibly check; it's very easy to try.
No connections besides power plug and one (or two) wires from header P8 to 
P9
Scenario 1: connect P8-43 to P9-30, plug in power, only power light comes 
on and BBB does not boot up
Scenario 2: connect P8-44 to P9-28, plug in power, only power light comes 
on and BBB does not boot up
Scenario 3: connect both P8-43 to P9-30 and P8-44 to P9-28, plug in power, 
power light and all 4 LEDs come on steady and BBB does not boot up.

Discussion:
1) doing these tests numerous times on 2 BBB's did not hurt either one of 
the boards I have, but this behavior is so strange that it might be risky; 
please don't be upset with me if it hurts your board.
2) uname -a gives Linux beaglebone 3.8.13-bone70 #1 SMP Fri Jan 23 02:14:42 
UTC 2015 armv7l GNU/Linux. My OS version is Debian wheezy 7.8
3) without wires connected, after booting and doing a 
>sudo cat /sys/kernel/debug/pinctrl/44e10800.pinmux/pins shows
...
pin 42 (44e108a8) 0000002f (this is P8-43 in mode 7 which should be gpio2_8)
pin 43 (44e108ac) 0000002f (this is P8-44 in mode 7 which should be gpio2_9)
...
pin 102 (44e10998) 00000027 (this is P9-30 in mode 7 which should be 
gpio3_17)
pin 103 (44e1099c) 00000027 (this is P9-28 in mode 7 which should be 
gpio3_16)

Therefore at boot, pins P8-43 and P8-44, without applying device trees, are 
both configured as inputs with pull-downs;
pins P9-30 and P9-28, without applying device trees, are both configured as 
inputs with pull_up/pull_down's disabled.

4) making the connections after boot does not have any discernible effects

5) It seems to me that having two gpio's connected together with both 
configured as inputs and one having a pull-down should not cause the BBB to 
freeze at boot.
6) It is also interesting that having two connections as in 5) causes 
different behavior; that is the boot process goes further to light all four 
LED's and then freezes.

Could someone check to see if they are getting similar behavior; I can't 
imagine that I am doing something real stupid with only a single wire 
connection; but I have previously done many rather stupid things so you 
never know (without verification).

Would someone in the expert category have some suggestions how to get 
around this problem; if we can't find a work around, months and months of 
work will be thrown away. For example, if we configured the device tree 
that is loaded at boot up, would it take precedence before the default pin 
mux that causes the freeze (if this happens to be the problem, currently we 
have no insight into what is causing this behavior).

Has anyone else seen similar problems (we may also have something funny 
with connections to P8-45 and P8-46 but have not tracked this down yet to 
simple scenarios.

I'm open to suggestions as we are currently stuck. Thanks.

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