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The problem could affect compliance requirements and operational needs at firms.
The service pack was distributed by Microsoft last autumn, but users have found that it blocks a number of files in older Excel, PowerPoint, Word and Corel Draw formats.
For instance, after installing the service pack, users have been unable to access Word 97-based documents.
In an advisory issued last month, Microsoft said, "After you install Office 2003 SP3, some Microsoft Office Excel 2003, Microsoft Office PowerPoint 2003, Microsoft Office Word 2003, and Corel Draw (.cdr) file formats are blocked.
"By default, these file formats are blocked because they are less secure. They may pose a risk to you."
However, many organisations need to have immediate access to documents in older formats for both operational and compliance reasons.
Microsoft, in its advisory, offers a complex workaround for the problem by manually modifying a system's registry, but if users get it wrong they risk losing all of their files.
Microsoft says, "Serious problems might occur if you modify the registry incorrectly by using Registry Editor or by using another method.
"These problems might require that you reinstall the operating system. Microsoft cannot guarantee that these problems can be solved. Modify the registry at your own risk."