Changes due to the implementation of the progress bar for opening a database have brought a nasty bug that can corrupt PGN files. When quitting the program with File->Quit, even if nothing was changed in the db, ChessX asks if changes have to be saved, and answering NO blocks the program for a while and corrupts the file (for each game, only headers and final result remain, not the moves). Quitting with File->Close followed by File->Quit appears to be both faster and safe.
Now solved.