I wish this weren’t being called a “punishment.” In my experience, this is aways due to an oversight or a simple error. What usually happens is that an author will receive an e-mail from the funding agency saying something like, “During an audit of your grant, we’ve noticed that such and such a paper has not been submitted to PMC. Failure to submit your article could result in a denial of future funding.” Then the author freaks out and e-mails the journal’s editorial office. Then an editor checks the funding disclosures and finds that the "NIH"or whatever box wasn’t checked. Then the error is fixed and the manuscript is deposited to PMC.
“Punishment” implies that authors are trying to avoid open access. I can’t imagine any author who, when faced with a clear and explicit choice, would choose to avoid open access.
