When you are observing data transfer issues with AUTO DMA channel,
1. Could you probe the GPIF flags (Eg: DMA Ready flag) and check if the flag is stuck at a particular logic.
2. If you have a USB protocol analyzer such as Teledyne Lecroy, take a USB trace and check if FX3 is sending NRDY packets.
Could you confirm if you are using a certified USB cable.
Use BulkLoop.exe Host Application provided in FX3 SDK and test with example projects for AUTO and AUTO_SIGNAL DMA channels :cyfxbulklpauto and cyfxbulklpautosig (C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.3\firmware\dma_examples) to check if you are observing any data transfer issues.