I just remembered where I got the "c.£3m" figure from..... this tweet from Tony Husband when the figures were published in March:
http://www.saintsweb.co.uk/showthread.php?43668-Saints-financial-figures&p=1639871#post1639871
My understanding is that the figures published in March weren't the regulatory annual company figures but disclosure of figures required by the Premier League (??). So, maybe that could account for figures included that are later in the financial year? Maybe, maybe not.
Anyway, that's where I got the figure from. Could be related to the BVI loan, or maybe not...?