Just to add to this, I'm in the same boat as simon - had posted about it here:
https://bitcointalksearch.org/topic/bitfinex-stopped-working-175210
As I didn't find this thread and couldn't work out how to get an invitation code to register for the bitfinex forums.
My loans were all at exactly the same rate (WAY over VIR) and I received about half the interest I should have got. Had exactly same loans still open yesterday and got the full amount (well about 5% under what I calc it should have been but near enough not to matter).
Not too fussed about it - with the returns I'm making some issues are inevitable. In fact they're desirable - as if there weren't occasional problems the site would be swamped in USD and we'd not get such good rates.
Here's mine for the record:
Currency Amount Rate (% per 365 days) * Expire in Auto-renew (lending offers) Actions
USD 29.19032581 1798.0% 12 months No Renew loan Notify
USD 2110.08319976 1798.0% 12 months No Renew loan Notify
USD 152.63 1798.0% 12 months No Renew loan Notify
USD 3638.7240986 1798.0% 12 months No Renew loan Notify
USD 2422.5448393 1798.0% 12 months No Renew loan Notify
And here's the interest payments for the last 2 days. Yesterday there WAS one more loan of a small amount for a short time and I have shorted BTC a few times - but only in small amounts and with it being BTCl oans ay tiny rates it would have had a trivial impact.
Interest Payment on wallet deposit 186.3949 8539.6236 13 Apr 01:10
Interest Payment on wallet deposit 370.3316 8723.5152 14 Apr 01:11
As I say, I'm not fussed about the small loss - but it definitely IS the case that some people got around half what they should have. Will provide my account name by PM/email if you (Raphael) want to look into it - but don't bother about it unless there's something you'd like to check out. Obviously I don't post my account name here.