Wow, sorry, how easy it is to misunderstand.
Now I hope you are talking about a standalone player and not one on your PC. Standalone do have setup options such as Pal NTSC or other which could affect frame counts and speed. For all I know your player may have a display setting which is adjustable.
Make sure this is set correctly first.
Also if you tried to flash the wrong bios then.....
Its only that I have experienced a similar problem on my 2 apex players but only when I modify the original DVD framerate. If the movie was 23.97 and I bumped it to 29.97 then I sometimes get weird readings under certain conditions (not yet identified). I have seen the opposite though a 5 minute clip shows up as 6 or 7 mins but stops at 5 minutes the way its supposed to.
I am still playing with the pulldown and up options to see if they are causing this effect but that's not my priority. Its on my list.
Right now all I know is I have yet to play a clip at 23.97 without a sound skip. I have to pull it up to 29.97 and it plays fine regardless of what the display says.