Heya
First post on this forum, so "hi all". I checked for similar older bug reports, this seems to be a new one.
I've got an ubuntu machine, and I'm using the nosound version (on which the game doesn't get frozen (as per other bug reports)).
In any case, when I start the executable (instead of the prepared shell scripts which create a new terminal) not from a terminal but from the window manager, the game doesn't load, and the player.dat gets erased. I've lost two already I believe. In any case, I worked out a simple workaround - I've removed execute permissions from the executable, and added a chmod +x doomrl and chmod -x doomrl before and after the execution of the game in the shell script. This way, accidentally running the executable is impossible, and no more player.dat files get erased. yipee.
I believe this might not even be completely 'the game's fault', but it doesn't matter that much to me anymore, since I got the workaround.