I was interested to read the JVCC Minutes, reported on the HMRC website (http://customs.hmrc.gov.uk/channelsPortalWebApp/channelsPortalWebApp.por...).
(My first thought was - why do HMRC take almost 5 months to publish these Minutes? And this is not unusual!)
The comment reads: "Some JVCC members commented that the new penalties rules have had an impact on the number of error corrections being submitted. They suggested that even where customers have made non-careless errors that can be corrected by making an adjustment to their VAT Return, in many cases disclosures were being made to HMRC as error corrections as a protective means of avoiding a possible penalty, resulting in increased bureaucracy for both taxpayers and HMRC."
This is also my experience. The guidance makes a distinction between an unprompted disclosure, and a prompted disclosure. An unprompted disclosure, with a clear explanation, and an accurate calculation of the errors identified, will result in a significantly reduced penalty, or perhaps no penalty at all. And so, when a taxpayer discovers an error, even if it can be adjusted on a Return, the preferred option is to submit a disclosure. I am also noticing that HMRC's Error Correction Team has a backlog.
(Second thought - why did HMRC not predict this obvious consequence of the new penalty rules?)
My advice - do submit a disclosure. And make sure the covering letter is clear. And, be patient!