I can report similiar issues. I can't believe the host system matters here.

Beaglebone kernel linux-image-4.1.12-ti-r29 works perfectly
Beaglebone kernel linux-image-4.1.15-ti-rt-r43 has flaw in USB0 as well as 
a flaw in another cape serial device...

The usb link is *almost* functional. The problem appears to be that the 
beaglebone doesn't receive ethernet packets over the usb ethernet device. 
It can send packets out that are picked up by my desktop ubuntu 14.04 LTS 
system. It is consistent with an RX interrupt mismatch on the beaglebone. 
RX count is always 1. TX goes up as expected.

-Dave

On Wednesday, January 27, 2016 at 9:44:09 PM UTC-6, [email protected] 
wrote:
>
> I experienced the same issue:
> BBB runs in 4.1.15-ti-rt-r43
> Host runs in 4.2.5-300.fc23.x86_64.
>
> I thought I had network setup issue in host PC. So I checked the route, 
> IP, net mask and gateway in host PC under 3.8 kernel, where host PC get 
> connected to USB gadget ethernet correctly.
>
> But even I manually applied this setting for 4.1.15-ti-rt-r43. The 
> connection is still broken. I wonder if/what DHCP server runs in 3.8? Is it 
> possible that kernel USB gadget driver is broken in 4.1?
>
> thanks,
> Ricky
>
>
> On Wednesday, December 9, 2015 at 12:11:10 PM UTC-5, Fabian Dalbert wrote:
>>
>> seems to have been a driver compatibility problem on the host side (linux 
>> mint 17.2, kernel 3.16). an update to linux mint 17.3 with kernel 3.19 
>> solved the problem.
>>
>> On Wednesday, December 9, 2015 at 9:13:47 AM UTC+1, Fabian Dalbert wrote:
>>>
>>> any ideas?
>>>
>>

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