I think you can be pretty sure that the STM32 isn't changing it's behaviour based on the type of CPU in the host system. Suggest you start looking at the OS, USB drivers, and USB hardware in the host.
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Also check your own hardware & software - it could be marginal such that you just happen to be ''lucky'' with one computer (the Intel one), and ''unlucky'' with the other...
A complex system that works is invariably found to have evolved from a simple system that worked.A complex system designed from scratch never works and cannot be patched up to make it work.