Simple Question. Duo to sony & panosonic

As with any firmware upgrade, sometimes things dont always go the way we hope an in your case it would appear sony have removed or broken support for some file types. I recall this happened with my S370 too but it was corrected with the following firmware update so not a big issue as this can happen with any makers devices (as recent dlna with duo v2 has shown) Your best bet to be sure would be to post on the sony support forums.
As for the upgrade, i have to say having had sony tvs an bluray players, media players an playstations for many many years ive never had an issue updating, the bluray players an tv usually take no more than a few mins to download and install new firmwares. Its highly likely the problems you mentioned are caused by other factors such as internet routing, connection speed. It is worth noting that if you are having issues downloading firmware directly to the device you can download them manually an install them manually.