Ok.. so here we go.
1. Regarding the first count on /acs-lang/admin those numbers include all the message keys, regardless of their status of deleted or not deleted.
2. In the Spanish package list index ( Lets focus on notifications ) we have:
Translated = 50, untranslated = 3 for a total of 53. Again, this numbers include all message keys ( whether they are deleted or not ).
3. Now, moving to the mesasge list filtered for notifications and locale es_ES. You have:
All ( 50 ) | Translated ( 50 ) | Untranslated (0) | Deleted (0).
I did check on the lang_messages table for the message keys that belong to the locale es_ES and package_ley notifications and, in effect, there are 50 entries; so.. where are those 3 message keys waiting to be translated? Well, it happen that those 3 message keys were deleted previously in the default locale ( en_US ) before they got to be translated into the locale es_ES. At first sight this is totally unclear from the numbers you get presented on this list. So I added an extra filter there, that will display to you those message keys deleted on the default locale that never got translated. So, you will see:
All ( 50 ) | Translated ( 50 ) | Untranslated (0) | Deleted (0) | Deleted on English (US) (3)
So you have a clear view of where those "missed" message keys.