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Yes, the 'wake up' only works within the first minute or so of the kindle sleeping.
I believe after that, the kindle goes into a 'deeper' sleep, and it won't be possible to wake up. (I might be wrong about this)
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Two things that might be worth checking on:
When the Kindle is on external power over the USB cable, that sets a "wake lock" flag in the kernel.
When the "wake lock" flag is set, the kernel never goes into "suspend".
So the additional USB hardware could be affecting that logic somehow.
In general, when the hardware present is changed, the kernel wakes from suspend to initialize (or uninitialize) the hardware support and updated its suspend image.
You can try that on your Linux PC, do a: "Suspend to RAM" on it -
Plug or un-Plug something from the USB bus.
So that might be leveraged somehow to wake (or even remote wake) the Kindle.
Details unknown.
On the Kindle, there is an 'always on' micro-controller monitoring the USB connector (among other things - like battery level).
Next to nothing has been posted about how that thing works.
But let your Kindle go to sleep - plug in USB cord from your PC -
Some combinations of Model and Firmware version immediately wake to give you the "Kindle charging, if you want to use ..." and export the USB storage.
Other combinations do not.
I never kept track of that behavior - if it doesn't wake up, I push the power button like everyone else.
