Weak internal controls sealed the fate of the finance chief and auditor PwC.
The pharmaceuticals company also canceled its 2016 financial guidance and delayed filing its fourth-quarter earnings report.
An Ernst & Young survey finds only 55% of CFOs are fully or somewhat confident their reports comply with all reporting needs.
The SEC also alleges American Growth Funding concealed from investors that many of its loans were non-performing.
The firm says the CFTC understated its lease obligations by about $212 million in 2014 and $194 million in 2015 because of an accounting error.
The settlement averts a trial of investor claims that PwC failed to properly audit the books of the largest operator of "feeder funds" to Madoff.
Does internal audit adequately cover the scope of the audit plan and report findings in a timely way?
Auditors will be required to file a new Form AP with the PCAOB, disclosing the name of the engagement partner.
The SEC alleges CPA Peter Messineo owned stakes in companies that the firm he worked for was auditing.
But Mary Jo White cautions that recent PCAOB inspections have found "significant deficiencies" and audit committees may be taking on too much work.