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Tracing lost USB bytes

I'm talking to a Masterguard UPS via USB. From a dump of an official MS-Win 
utility talking to it I know that I have to send commands to vendor specific 
endpoint 0D and replies are arriving in chunks of three to four bytes.
Once every few tries, communication fails because the first (three-byte) 
chunk of the reply is missing. From a ktrace/kdump -R output I know that 
in the failing case, the first read() takes slightly (in the order of 10ms) 
longer than in the working case. After that, every chunk (three or four bytes)
takes 16ms to read and nothing more seems to be missing.

Any way to debug this? Does it ring a bell to someone?

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