We are currently (Confluence 4.3.2) shipping PDFBox 1.6.0.

Attaching certain PDF files, can affect performance with the following error in the logs:

ERROR [scheduler_Worker-2] [apache.pdfbox.filter.FlateFilter] decode Stop reading corrupt stream.

Upgrading to PDFBox 1.7.1 solved the issue, even though I could not find any related issue in PDFBox issue tracker related to this problem and fixed between those versions.