Thanks everybody for your answers. Summarizing this case I'm commenting the actions we've taking, the results and our further plans for solve de problem:
*We applied by hand many of the patches documented in tracker. Some of them didn't worked, specially the ones which were applied to mdl_grades_history operation. And that was because the database was corrupted. Fortunately we could fix this problem.
*We did Mysql tuning, and the performance improved. But not as users demand. Well after some weeks of malfunction they are impatient.
*The next change we'll do is converting the database to InnoDB. And test if it's better.
Right now we have the opportunity for an actualization to 1.9.9. So in the next weeks we will test the same environment with the newer version. I'll be glad to post the results as closure of this case.
Thank you all for your your comments.