Somewhat hesitant about this but there is firmware update for your 5900 and in fact you may already have the latest update found here:
The reason being, I don't do firmware updates myself unless it is a special case.
Indeed it may fix somethings and then break others.
Not that this will help your situation but I bought a cheap LG BPM33 and indeed it is very cheap, especially compared to my old panny 2011 model 310.
Yet it does play rewrapped blu-ray files into mkv well...doesn't do the chapters but seems to pause well enough and it has an onscreen info/menu page that can advance the movie easily in 1 minute increments.
Through the keypad, any increment can be entered and it advances to that position.
My inboard media player in my Samsung tv does similar to your BD player in that if it is paused to long, it will drop the connection to the hard drive but it has a feature that will allow it to advance to the last previous play position, which is nice.
But it doesn't do chapters in mkv either, it can advance in fast play increments.
My idea is that these media players are a simple form of a linux distro though I suppose Samsung could make their own operating system for media play.
All of these players are somewhat after thoughts in that they can be picky in what they play and the feature sets are generally limited.
There is a media player that I was tempted to buy but it is around 140+ yet it supposed to play about anything one can throw at it.