The bug prevents the Jira from finding files on vendor branches in the CVS logs.
Example CVS log of one file of the ones above do have the following CVS log entries:

[eckmac:~/RPSEvaSysCustomCode] ecke% cvs log -N raytheon/server.php5

RCS file: /usr/local/cvsrep/RPSEvaSysCustomCode/raytheon/server.php5,v
Working file: raytheon/server.php5
head: 1.1
branch: 1.1.1
locks: strict
access list:
keyword substitution: kv
total revisions: 7; selected revisions: 7
description:
----------------------------
revision 1.1
date: 2008/02/08 10:57:12; author: rainecke; state: Exp;
branches: 1.1.1;
Ecke prepended commit message to add Jira issue: GMLMS-3190.
Initial revision
----------------------------
revision 1.1.1.6
date: 2008/05/22 10:06:32; author: rainecke; state: Exp; lines: +1 -1
Update received from Electric Paper.
----------------------------
revision 1.1.1.5
date: 2008/05/20 09:47:24; author: rainecke; state: Exp; lines: +5 -1
Update received from Electric Paper.
----------------------------
revision 1.1.1.4
date: 2008/04/01 10:00:12; author: rainecke; state: Exp; lines: +1 -2
Ecke prepended commit message to add Jira issue: GMLMS-3190.
Update received from Electric Paper.
----------------------------
revision 1.1.1.3
date: 2008/03/18 16:40:38; author: rainecke; state: Exp; lines: +5 -1
Ecke prepended commit message to add Jira issue: GMLMS-3190.
Update received from Electric Paper.
----------------------------
revision 1.1.1.2
date: 2008/02/14 09:20:39; author: rainecke; state: Exp; lines: +8 -0
Ecke prepended commit message to add Jira issue: GMLMS-3190.
Update received from Electric Paper.
----------------------------
revision 1.1.1.1
date: 2008/02/08 10:57:12; author: rainecke; state: Exp; lines: +0 -0
Ecke prepended commit message to add Jira issue: GMLMS-3190.
Initial import of vendor code.
=============================================================================

All issues mentioning GMLMS-3190 should show in the Version Control area of Jira. They don't.