NIH recommend Authors and PI's use their My NCBI account bibliography to manage compliance, however there is another system the "compliance monitor" that enables eRA Commons account holders to run a search for all papers that have one of your awards associated and that are out of compliance.
The NIH have published a user guide to the Public Access Compliance Monitor (PACM). The Becker medical library have produced a one page guide on how to interpret the Public Access Compliance Monitor (PACM) report.
Log into the compliance monitor by clicking the Login via MyNCBI link, then click the NIH Login link to sign in with your eRA Commons account.
In the compliance monitor you can set a date range for which you want to retrieve articles, say April 2008 (when the policy was initiated) to present.
Click the number under the "Noncompliant" column.
Click "PI Name" to sort alphabetically, and scroll down to your name.
You may find papers that are not on your MyNCBI bibliography, but that show up in the compliance monitor because the paper has been associated with your NIH grant number.
Check if there is a number in the NIHMSID column. If there is a number, the paper has been deposited in the NIHMS but is waiting for the author to authorise the text/deposit - they will have received an email to do so. You can email the NIH public access helpdesk at PublicAccess@nih.gov to ask them to reassign the article submission in the NIHMS to another author.
If there is no number in the NIHMSID column, check if the journal publisher is supposed to deposit the text, or you can begin the deposit your self or via your delegate through your MyNCBI bibliography or directly through the NIHMS.