Works for me on Mac OS X.

timer-example.log

$ timer Boring Customer \#4
Name your timer? wordpress
14:12 Started timer wordpress
0s      > wait
14:12 Paused timer wordpress
9s      + ; 5-minute configuration
9s      + 
14:22 Started timer wordpress
22m15s  > x
14:45 Total time wordpress 22m15s
; session time 32m57s
Name your timer? 
14:55 Started timer
0s      > x
14:56 Total time timer 18s
; session time 0m18s
Name your timer? x

2014-01-09  Boring Customer #4
       wordpress  22m15s ; 5-minute configuration
           timer  18s    ;
22m33s Total time
$ _

timer.sh

#!/usr/bin/env MAIN= bash
# runs a named timer that you can pause, time after time
# will print a ledger-like entry on Ctrl-C
#
# http://www.gnu.org/software/bash/manual/bashref.html
# 

timer () { # DEFAULT_ACCOUNT_NAME

   time_fmt () {  # prints SECONDS in 0h0m0s format
      unset H M
      local H M
      [[ 60 -gt $1 ]] && printf "${1}s" \
      || (M=$(($1 / 60))
         [[ 60 -gt $M ]] && printf "${M}m$(($1 - $M * 60))s" \
         || (H=$(($M / 60))
            printf "${H}h$(($M - $H * 60))m$(($1 - $M * 60))s"))
   }
   START_TIME=$(date +%s)

   date_fmt () {  # prints SECONDS in YY-MM-DD format
      date -j -r ${1:-$START_TIME} +%Y-%m-%d
   }
   sum_nums () {  # sums up numbers from STDIN
      awk -v RS=' ' '{sum+=$0} END {print sum}'
   }
   DEF_ACC=$@
   COUNTS=() NAMES=() COMMENTS=()
   MARK=`tput setaf 7` PARK=`tput setaf 13` BARK=`tput setaf 4` YELL=`tput setaf 3` UMRK=`tput sgr0`

   print_result () {
      echo
      echo $MARK`date_fmt`$UMRK"  $DEF_ACC"
      local I=0 NAME

      for AMT in ${COUNTS[@]}; do
         NAME="${NAMES[$I]:-timer}"
         while (( ${#NAME} < 16 )); do
            NAME=" $NAME"
         done
         echo "$NAME  "$MARK`time_fmt $AMT`$UMRK$'\t'\;${COMMENTS[$I]}
         I=$(($I + 1))
      done
      echo $(time_fmt `sum_nums <<< "${COUNTS[@]}"`) ${YELL}Total time$UMRK >&2
      unset START_TIME DEF_ACC COUNTS NAMES COMMENTS \
            MARK PARK BARK YELL UMRK \
            time_fmt date_fmt sum_nums input_loop print_result
   }
   trap "print_result" TERM EXIT

   input_loop () {
      echo $MARK`date +%H:%M`$UMRK Started timer $@ >&2
      local TIME=$(date +%s) SHOW=0 COUNT=0 COMMENT
      local TIME_DELTA=$TIME STOP PAUSE STATE=

      while read -p `time_fmt $SHOW`$'\t'$BARK${STATE:->}$UMRK' ' CMD; do
         [[ $CMD = [.xX]* ]] && STOP=1
         [[ -n $CMD && $CMD != [.xX]* ]] && PAUSE=1 || PAUSE=
         [[ $CMD = [\;#]* ]] && COMMENT+=$'\n'"${CMD#[\;#]}"

         TIME=$(date +%s)
         [[ $PAUSE ]] && {
            [[ -z $STATE ]] && {
               echo $PARK`date +%H:%M`$UMRK Paused timer $@ >&2
               COUNT=$(($TIME - $TIME_DELTA + $COUNT))
            }
            STATE='+'
            SHOW=$COUNT

         } || {
            [[ $STOP ]] && {
               [[ -z $STATE ]] && COUNT=$(($TIME - $TIME_DELTA + $COUNT))
               TIME=$@
               TIME=$MARK${TIME:-timer}$UMRK
               echo `date +%H:%M` Total time $TIME $YELL`time_fmt $COUNT`$UMRK >&2
               COUNTS+=($COUNT)
               NAMES+=( "$@" )
               COMMENTS+=( "${COMMENT}" )
               break
            }
            [[ $STATE ]] && {
               echo $MARK`date +%H:%M`$UMRK Started timer $1 >&2
               STATE=
               TIME_DELTA=$TIME
            } || tput cuu1
            SHOW=$(($TIME - $TIME_DELTA + $COUNT))
         }
      done
   }

   user_interrupt () {
      echo -n $'\nStop and exit the timer? ([y]/n) ' >&2
      read ANS
      [[ ${ANS:-y} = [yY] ]] && exit
   }
   trap 'user_interrupt' INT


   local TIMEFORMAT='; session time %0lR'
   while true; do
      read -p 'Name your timer? ' TIMER || {
         echo >&2 ; break
      }
      [[ $TIMER = [.xX] ]] && break
      time input_loop "$TIMER"
   done
}


## run if not sourced from other script
#  TODO: make it function when sourced
[[ ${MAIN-RUN} ]] || {
   (( $# == 1 )) && [[ $1 = *-h* ]] && {
      cat <<HELP
Usage: `basename ${BASH_SOURCE[0]}` [DEFAULT_ACCOUNT]

Account name is optional; pause the timer by typing,
start it again with blank line, end it with . or x
To add a comment start line with ; or #, comments pause.
Will print ledger-style entry upon exiting.
HELP
      exit
   }
   timer $@
}