flacs renamed to mp3 is a good alternative to play them, my sammy bluray also does the same way
for external sub like srt files, make sure you name the srt file same as video file and they are both in same folder, but even my bluray player does not show sub many a times, you needs to get a proper media player like himedia on which every subtitle is shown also you can adjust their look and feel, font size placement etc which is quite handy
slow bowsing with many folders again not only your bdplayer issue
and for many mkv and mp4 not played, I already mentioned that sammy is the best in codec support, sony is poor but one thing sony can do which sammy cannot is it can play a 3D file from usb, you ask the retailer to give you their demo sony 3D file on a usb then u try playing it, its amazing
good to know you enjoying ur player
yeah sony PQ is quite impressive
and what was the price you got it for ?