I am having a similar issue to what is described in the post from Feb 2018 (https://renesasrulz.com/synergy/f/synergy---forum/10043/problem-with-usb-transfer-speed).
I have a thread which reads from the SPI roughly 10K samples a second. The sampling does not have any issues in my application until I attempt to write to the USB using fx_file_write. During the fx_file_write I start missing samples, I have not yet determined if it is caused by the interrupt being disabled or filex preventing my thread from executing. I have confirmed that my interrupt and thread priority are higher than the filex. Unfortunately it doesn't look like I have access to the filex source to debug the issue. I have tried with and without DTC/DMA with no change. Any ideas as to why fx_file_write would prevent high priority threads from executing?
Thanks.