Here I am, over a year and a half later looking for help with a similar issue.
I just tried this fix suggested by Joseph Rézeau centuries ago and it seems to work.
In Moodle 1.6+
In file \mod\journal\report.php, line 86 replace
$entrybyuser[$entry->userid]->comment = $vals['c'];
with
$entrybyuser[$entry->userid]->comment = stripslashes($vals['c']);
See Joseph's post:
http://moodle.org/mod/forum/discuss.php?d=53582#p244694
Now let's see if I can fix the Questionnaire module where the same problem was just reported.
FL