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The penalty regieme for late payment of CIS is changing from November:

http://www.hmrc.gov.uk/cis/news/penalties.htm

“The first return falling within the new penalty regime will be the return for the month ending 5 November 2011.

“The following penalties will apply to that return and all subsequent months’ returns that are not filed or filed late:

•A fixed penalty of £100 immediately a return is late.
•A second, fixed penalty of £200, two months after the filing date if the return is still outstanding.
•If the return is still outstanding six months after the issue of the first penalty, a tax-geared penalty is charged which is the greater of £300 or 5% of the amount of deductions shown on the return.
•If the return is still outstanding twelve months after the issue of the first penalty, a further tax-geared penalty is charged which is the greater of £300 or 5% of the amount of deductions shown on the return. Higher levels of penalty apply where, as a result of the failure to file the return on time, information has been deliberately withheld. “