I've put my reply in-line with a copy of your questions. My text is dark red to make it easier to follow. Again, thank you for your attention to this.

  • OS of the master node and slave nodes.

    - Master and slaves are Windows Server 2008 R2 Standard.
  • Outline of your build process. For example, running maven, running gcc, or running other native process.
    • I think whether builds are performed in Java or native processes can affect this problem.

      - There are 561 defined projects that have built in the past two weeks, so I'll have to generalize.
      - Our projects are 80 to 90% "free-style software projects", the rest being "multi-configuration projects".
      - We use Git and Gerrit for source code management, however some projects select "none" and use multiple git repos.
      - Our build-steps are normally "execute shell" or "execute windows batch command"
      - Overwhelmingly we use WAF for building C/C++ source files; that's both with licensed compilers and "free" compilers.
      - For authorization, we use "project-based Matrix Authorization Strategy" with 40 defined users plus anonymous. Some projects also enable project-based security.
  • How much log outputs? I think the size of whole log and the time builds take will be helpful.
    • I think much log outputs may trigger the problem.

      - Quick survey says... 20,000 to 40,000 lines of text for our most popular projects.
      - These builds average 25 to 50 minutes; strangely, the quicker projects tend to generate more logs.
  • Can you see what process gets slow in builds?
    • If building processes outputs timestamps, please compare them before and after downgrading build-timeout plugin.
    • If you installed Timestampler plugin, please compare timestamps in console outputs.
      • Timestamps logged with timestampler-plugin may differ from the activity of the building process as they can be buffered and delayed.
    • If you don't have timestamper-plugin installed, you'd better not install that as that plugin also captures log output and may cause the same problem.

      - Plugin timestamper is installed, but only some projects use it. However, the builds in question are no longer saved because they're so long ago, therefore I cannot examine them with the timestamps.
      - I do have some data captured in a database about those builds. That's data like job-name, build-number, result, build-duration, and interestingly, excerpts from the logs for failed/aborted builds.
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