Mail Per User Quotas Not Working

Question

We just migrated from 10.9 server to the new 10.10 server and noticed that our per user mail quotas were no longer working.  If I change the Server app - Mail setting - to have a global mail quota on it work, however, we have a few accounts that we need to leave unlimited and the per user quota will not override the global quota.  So far we have had to leave the global quota disabled because of this.
Even without global quota turned off - trying to set per user mail limits is still not working.  We are changing it thru the Server app and clicking users - selecting a user - then select edit mail options - and changing the setting for the limit size.  No matter what we set it to - it will not work.
Does anyone know what command or how to change the per user quota limits from the command line?  I found that Dovecotadm quota -u username  shows you what the quota is, but I am stumped as how to change it via a command line or thru another method since the server app is not working.
Any help would be appreciated!
ps. Also posted my doveconf -n file below, but I am missing if there is anything not configured properly.
bash-3.2# dovecot -n
bash: dovecot: command not found
bash-3.2# doveconf -n
# 2.2.5: /Library/Server/Mail/Config/dovecot/dovecot.conf
# OS: Darwin 14.1.0 x86_64  hfs
aps_topic = com.apple.mail.XServer.a1c54f6d-f4ad-4431-b882-0f11570dd637
auth_mechanisms = cram-md5 plain login
auth_socket_path = /var/run/dovecot/auth-userdb
auth_username_format = %n
debug_log_path = /Library/Logs/Mail/mail-debug.log
default_internal_user = _dovecot
default_login_user = _dovenull
disable_plaintext_auth = no
first_valid_gid = 6
first_valid_uid = 6
imap_id_log = *
imap_id_send = "name" * "version" *
imap_urlauth_submit_user = submit
info_log_path = /Library/Logs/Mail/mail-info.log
log_path = /Library/Logs/Mail/mail-err.log
login_log_format_elements = user=<%u> method=%m rip=%r lip=%l mpid=%e %c
mail_access_groups = mail
mail_attribute_dict = file:/Library/Server/Mail/Data/attributes/attributes.dict
mail_location = maildir:/Library/Server/Mail/Data/mail/%u
mail_log_prefix = "%s(pid %p user %u): "
mail_plugins = quota zlib acl fts fts_sk
managesieve_notify_capability = mailto
managesieve_sieve_capability = fileinto reject envelope encoded-character vacation subaddress comparator-i;ascii-numeric relational regex imap4flags copy include variables body enotify environment mailbox date ihave
mdbox_rotate_size = 200 M
namespace acl-mailboxes {
  list = children
  location = maildir:/Library/Server/Mail/Data/mail/users/%%u:INDEX=/Library/Server/Mail/Dat a/mail/shared/%%u
  prefix = shared.%%u.
  separator = .
  subscriptions = no
  type = shared
namespace inbox {
  inbox = yes
  location =
  mailbox Drafts {
    special_use = \Drafts
  mailbox Junk {
    special_use = \Junk
  mailbox Sent {
    special_use = \Sent
  mailbox "Sent Messages" {
    special_use = \Sent
  mailbox Trash {
    special_use = \Trash
  prefix =
namespace list-archives {
  list = children
  location = maildir:/Library/Server/Mail/Data/listserver/messages/archive/lists/%%u:INDEX=/ Library/Server/Mail/Data/listserver/messages/archive/shared/%%u
  prefix = archives.%%u.
  separator = .
  subscriptions = no
  type = shared
passdb {
  driver = od
passdb {
  args = /Library/Server/Mail/Config/dovecot/submit.passdb
  driver = passwd-file
plugin {
  acl = vfile:/Library/Server/Mail/Config/dovecot/global-acls:cache_secs=300
  acl_shared_dict = file:/Library/Server/Mail/Data/shared/shared-mailboxes
  fts = sk
  quota = maildir:User quota
  quota_warning = storage=100%% quota-exceeded %u
  quota_warning2 = storage=85%% quota-warning %u
  sieve = /Library/Server/Mail/Data/rules/%u/dovecot.sieve
  sieve_dir = /Library/Server/Mail/Data/rules/%u
  stats_refresh = 30 secs
  stats_track_cmds = yes
protocols = imap lmtp sieve pop3
quota_full_tempfail = yes
service auth {
  extra_groups = _keytabusers
  idle_kill = 15 mins
  unix_listener auth-userdb {
    user = _dovecot
service dns_client {
  unix_listener dns-client {
    mode = 0600
service imap-login {
  inet_listener imap {
    port = 143
  inet_listener imaps {
    port = 993
    ssl = yes
  service_count = 0
service imap {
  client_limit = 5
  process_limit = 200
  service_count = 0
service indexer-worker {
  user = _dovecot
service lmtp {
  unix_listener lmtp {
    mode = 0600
service managesieve-login {
  inet_listener sieve {
    port = 4190
service pop3-login {
  inet_listener pop3 {
    port = 110
  inet_listener pop3s {
    port = 995
    ssl = yes
service pop3 {
  client_limit = 5
  process_limit = 200
  service_count = 0
service quota-exceeded {
  executable = script /Applications/Server.app/Contents/ServerRoot/usr/libexec/dovecot/quota-exceeded .sh
  unix_listener quota-exceeded {
    group = mail
    mode = 0660
    user = _dovecot
  user = _dovecot
service quota-warning {
  executable = script /Applications/Server.app/Contents/ServerRoot/usr/libexec/dovecot/quota-warning. sh
  unix_listener quota-warning {
    group = mail
    mode = 0660
    user = _dovecot
  user = _dovecot
service stats {
  fifo_listener stats-mail {
    mode = 0600
    user = _dovecot
ssl = required
ssl_ca = </etc/certificates/mail.maxxx.com.3524D1A33970C65E8A8DFF78E757DDE3C66AED10.chai n.pem
ssl_cert = </etc/certificates/mail.maxxx.com.3524D1A33970C65E8A8DFF78E757DDE3C66AED10.cert .pem
ssl_cipher_list = ALL:!LOW:!SSLv2:!EXP:!aNULL:!ADH:!eNULL
ssl_key = </etc/certificates/mail.maxxx.com.3524D1A33970C65E8A8DFF78E757DDE3C66AED10.key. pem
ssl_key_path = /etc/certificates/mail.maxxx.com.3524D1A33970C65E8A8DFF78E757DDE3C66AED10.key.p em
userdb {
  args = partition=/Library/Server/Mail/Config/dovecot/partition_map.conf global_quota=0 enforce_quotas=yes
  driver = od
userdb {
  args = /Library/Server/Mail/Config/dovecot/submit.passdb
  driver = passwd-file
verbose_proctitle = yes
protocol lmtp {
  mail_plugins = quota zlib acl fts fts_sk sieve
protocol lda {
  mail_plugins = quota zlib acl fts fts_sk sieve push_notify
protocol imap {
  mail_max_userip_connections = 20
  mail_plugins = quota zlib acl fts fts_sk imap_acl imap_quota imap_zlib
protocol pop3 {
  mail_max_userip_connections = 6

Answer 1

I guess the problem didn't resolve itself, rather it has revealed that it is intermittent (my favorite kind).
What could made a message sent to a legitimate alias username not get picked up during the imap connection. I know the smtp server accepted the message (see logs above).