Reviving this thread, not sure I solved the file format issue, but will say no files played in my system from flash drive through either AVR or BDP sound very good, no matter how they are ripped or which format. Have switched to AIFF vs FLAC based on my interpretation of advice on Steve's website. In any case, I am beginning to think it is the USB bus implementation for flash drive on both AVR and BDP compared with any other digital input, at least on the AVR.
Reason for that consideration is I bought an Arcam irdac for two channel audio in this system and it sounds very good to my ears with any input used: USB B, iPhone, toslink, you name it. These are the exact same files as on the flash drive, just played on my laptop with JRiver or my iPhone 5s instead through the irdac. It supposedly uses asynchronous USB solution supplied by DCS. Whatever, it sounds terrific.
Next question related to last bit of this thread above on switching versus linear power supplies. I am contemplating replacing stocks wall wart for irdac with linear PS. Steve says great switching PS beats great linear PS. Doubt I can find top flight switching PS at appropriate price point, and doubt stock unit for Arcam falls into this category. So what then is a reasonable upgrade for irdac?
Others have recommended Teddy Pardo Linear PS, Main Cables R Us advertises extensively on eBay, Custom Hifi Cables makes an interesting looking unit, and Paul Hynes who designed the regulator for the Overdrive SE makes a stand alone unit for the irdac as well. All are in the same ball park in terms of cost ($250-$350 USD), and all have champions that swear the custom power supplies improve performance of small DACs over stock wall warts. In terms of a linear supply to improve performance of my irdac, what do you recommend?