Not sure if we should put an index into this database... but the following fixed the issue:

CREATE NONCLUSTERED INDEX [IX_MSRepl_Commands_Art_Pub] ON [dbo].[MSrepl_commands]

(

[article_id] ASC,

[publisher_database_id] ASC

)

INCLUDE ( [xact_seqno]) WITH (PAD_INDEX = OFF, STATISTICS_NORECOMPUTE = ON, SORT_IN_TEMPDB = OFF, IGNORE_DUP_KEY = OFF, DROP_EXISTING = OFF, ONLINE = OFF, ALLOW_ROW_LOCKS = ON, ALLOW_PAGE_LOCKS = ON) ON [PRIMARY]

GO