A quick Google unearths the following:
From the Bookseller, 13.6.08: reports that the CC is to investigate St. Stephen the Great following the filing for bankruptcy in the US: A spokesman for the Charity Commission said: “We are currently considering whether this raises any issues for the Charity Commission to take forward.” Haven't heard any more about this since. I don't know if the Bookseller followed it up - there doesn't seem to be any more about this in their other articles on the saga, though the comment on this one is very interesting for other reasons.
(The Bookseller article was reported by Dave Walker on June 13th 2008, and there were 11 comments but I don't think these are accessible any more. This is one of the many sites that have reposted some of Daves stuff, if you scroll down you can find the relevant post, but it doesn't add any more information. )
A comment on Ruth Gledhills blog roughly 12 months ago noted that the Charity Commission had also investigated the sale of the bookshops to SSG by SPCK, and found it to be within the rules. It also explains why there is both an SSG and an SSG Charitable Trust registered with the Charity Commissioners - the commenter says that this was at the CC's insistence, one charity to run the bookshops, the other to purchase churches. Though if they are 2 separate charities, the storage of bookshop fittings in an SSG church seems to blur the boundaries somewhat.
So the CC already have a small file on SSG, but there's no mention in these reports of investigations into Gift Aid, filing of accounts, the relation of SSG to ENC etc., so at least Mondays letter won't be wasting their time.