To me these lines in rcS-late look like the culprit:
# Remove duplicate commas from variables
mydocs_opts=`echo $mydocs_opts | sed ':l;s/,,/,/g;tl;s/^,//;s/,$//'`
home_opts=`echo $home_opts | sed ':l;s/,,/,/g;tl;s/^,//;s/,$//'`
as following lines
[ -z "$mydocs_opts" ] && mydocs_opts=defaults
[ -z "$home_opts" ] && home_opts=defaults
will write "defaults" and not the correct options read from mount-opts.
And iirc I believe I read something about exactly those sed to be corrected/adapted or similar (maybe I am wrong and it was just about swap partitions).