Its good that the application closes the terminals at the end of the compilation - thanks. Still, the script didn't produced the references. This time I cleaned all the old files and it looks as if it didn't produce the bibtex files (.bbl and .blg files). Checked a more complicated file with the references listed in the main .tex document - this time the refs came out OK and the html file looks very nice. It looks as if the script doesn't recognize some of the files (.sty at least) which are located in the same folder as the main .tex document (I had to insert the full phath manually).