I have just ported Linux kernel 3.17.3 to our board. This stops the system going into OTG probing when the g_ether module is loaded. It still does a single OTG probe when initially loaded but there is no every 2 seconds probe. If this fixes things for all USB modules, I don't know and I don't know in which kernel version between 3.12.10 and 3.17.3 it was fixed. Not sure if the vanilla kernel 3.17.3 will work on the Beaglebone.
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