The 2009 entry vacancy we currently have is for a position in our investment team. Our 2010 entry holds both investment and accounting vacancies.
You say "clearly there must be more than one vacancy." Why "clearly"? It's not clear to me.
Do you think the 2010 vacancies are plural because they are in two categories?? (only one vacancy in each category)
Maybe his English is not too good. The 2009 statement is all singular: "[it] is for a position"
I suppose it's possible he's speaking of "the position" as a job classification (singular) while 2010 has openings in two classifications (plural). In this case he may be using "vacancy" as uncountable noun.
"We have a vacancy of two openings for the position of accountant." Does that make sense?
I don't think a native English speaking American would put it this way, but it's not ungrammatical.