Pencheff
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Pencheff's post in Legacy kernel - USB 2.0 ports "HC died" fix ? was marked as the answerNevermind, it turns out not to be a kernel problem. Leaving details about what was wrong, if anyone else has similar issues.
I have a custom USB HID device that gets accessed every 3-4 seconds by an app, which uses libusb. The libusb has 2 implementations - libusb-1.0 and hidraw. It turns out libusb-1.0 implementation was causing the host controller issues, funny it happened only with legacy kernels.
The problems went away when I switched to the hidraw implementation.