Hey Mark,
thanks for the tips. In Wireshark, the addresses (if I understood correctly) are formed as BUS.DEVICE.ENDPOINT. That menas 1.3.* and 1.1.* are different devices and from the pictures, I'd say the board is enumerated with the address 1.1.*.
Wireshark indeed doesn't show much of the communication and I unfortunately don't have a Hardware USB Analyzer. I found, though, another tool that gave me better results: Microsoft Message Analyzer. I redid the experiments with this tools and got the following results:
My firmware
During enumeration, I get some problematic packages (6 packages). They show problems with Stall commands followed by endpoint halt command, but enumeration goes fine.

After enumeration, communication goes on as it was on the Wireshark experiments (several Bulk In and Bulk Out Transfers), until eventually I get the following error: Status Babble. This makes windows close the endpoint and open it with a different address (??) - I don't really understand that, but I do understand there is an error with the Status message.

Your Firmware (initial one, without FreeRTOS)
The same Stall problems during enumeration appear, but this time I can see 9 times the problem.

During execution, your application too get some other stall problems followed by endpoint halt, but I can't see any status babble problems.

I'll go further into this status babble problem, as it seems to be causing the problem (bus reset).
I attached the trace files.
Cheers,
Bruno