The problem still exists. We have the same thing here. If a project ID ends with the name of another project ID, the issue tracker is unable to make the difference in the workflow log.
example in our case, we have a project keyed 'INTRANET' (the intranet interface, for end users) and another keyed 'RMIINTRANET' which is used to track programming problem in the RMI_intranet cvs module.
For every issue in INTRANET project, the commit log show also the commit for RMIINTRANET issues having same numer.
For example, here is the output for issue 'INTRANET-15':
Validé (committed) par davidd dans '1' module dissco-02.RMI_intranet
Updated translations file (INTRANET-15)
MODIFY webapp/WEB-INF/classes/resources/mission_nl.properties Rev. 1.10 (+19 -19 lines)
Validé (committed) par davidd dans '11' module dissco-02.RMI_intranet
Updated Hibernate to use a container datasource, share this datasource with the one used by OSWorkflow, changed name of those datasources, added connection validation, updated idle and max connection to prevent deadlocks. This is a fix for RMIINTRANET-15
MODIFY webapp/WEB-INF/osworkflow.xml Rev. 1.3 (+1 -1 lines)
MODIFY configSets/rmibeta/META-INF/context.xml Rev. 1.2 (+11 -5 lines)
The property is jira.option.key.detection.backwards.compatible and need to be set to true if backwards compatibility is required.