eXo JCR is throwing "Duplicate entry" and "(update) Property not found xxx. Probably was deleted by another session" errors in Portal

Issue

We are seeing errors like this in our Portal server:

Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry 'collaboration0' for key 'JCR_IDX_SVALUE_PROPERTY'

and

Caused by: org.exoplatform.services.jcr.impl.storage.JCRInvalidItemStateException: (update) Property not found []:1[]sites content:1[]live:1[]foo:1[]bar:1. Probably was deleted by another session 
at org.exoplatform.services.jcr.impl.storage.jdbc.optimisation.CQJDBCStorageConnection.update(CQJDBCStorageConnection.java:490)

and

Caused by: javax.jcr.RepositoryException: [collaboration] EDIT PROPERTY. Item already exists. But update errors. []:1[]sites content:1[]live:1[]foo:1[]bar:1 
Cause >>>> Lock wait timeout exceeded; try restarting transaction: Lock wait timeout exceeded; try restarting transaction