Strange behavior of default application assignment

Some of our RHEL 5.10 servers show strange behavior in assigning a default application to a specific MIME-Type, say application/pdf. I expect /usr/share/applications/defaults.list to set the standard application for each MIME-Type. This works for most of our servers, but some are dealing different...

When I cd to /usr/share/applications on any machine and look into defaults.list, it says:

root@red1:1258> grep pdf defaults.list 
application/pdf=AdobeReader.desktop

AdobeReader.desktop is existing and is world readable on each machine:

root@red1:1259> ls -l AdobeReader.desktop 
-rw-r--r-- 1 root root 371 23. Sep 07:35 AdobeReader.desktop

Therefore, Adobe Reader should be the default application for PDF files. Let's check with xdg tools:

root@red1:1260> xdg-mime query default application/pdf
AdobeReader.desktop

OK, but files seem to get opened via the Gnome Virtual File System, which seems to ignore the default on the machines in question:

root@red1:1261> gnomevfs-info /some/path/MA.pdf 
Name              : MA.pdf
Type              : Regular
MIME type         : application/pdf
Default app       : evince.desktop
Size              : 34357
Blocks            : 72
I/O block size    : 32768
Local             : YES
SUID              : NO
SGID              : NO
Sticky            : NO
Permissions       : 600600
Link count        : 1
UID               : 515
GID               : 100
Access time       : Fri Sep 27 16:46:13 2013
Modification time : Fri Sep 27 16:46:14 2013
Change time       : Sat Jan 25 14:50:15 2014
Device #          : 19
Inode #           : 92410160
Readable          : YES
Writable          : YES
Executable        : NO

Gnome VFS seems to default to the first application entry in mimeinfo.cache, which is evince on this machine:

root@red1:1262> grep pdf mimeinfo.cache 
application/pdf=evince.desktop;AdobeReader.desktop;fedora-gv.desktop;

Of course I can alter the sequence of applications in mimeinfo.cache, which immediately influences the default application. But since the cache file is newly generated when installing or uninstalling packages, this would be necessary quite frequently.

Therefore I kindly ask if anybody can point me a way to
- make Gnome VFS respect the default application, or at least
- influence the application sequence in mimeinfo.cache in a persistent way.

Any help would be highly appreciated.