When you raise the threshold value you're hiding PageSpeed's warnings,
but you're not fixing the underlying problem of file reads taking too
long. PageSpeed uses blocking file reads, and was built around an
assumption that these would generally complete quickly. While a file
read is happening PageSpeed can't do anything else, and so if those
are very slow PageSpeed gets behind.
It sounds like in your case you have a file system that is sometimes
very slow, and PageSpeed is giving you "Slow read operation on file"
and "Waiting for completion of URL" errors to let you know about the
problems it's having. To fix this you could speed up the file system
or keep PageSpeed from needing the filesystem (by switching our cache
to memcached and/or turning off LoadFromFile.
(This is different than the problem you were having with 1.9.32.3,
because the wait times are much lower, even though the error messages
are similar.)
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https://groups.google.com/d/msgid/mod-pagespeed-discuss/CAOjCk%3DkDfOGE%3Dj2gZFd3WVW2BRb_fQWAwkrszXx3%2BrRjWyyiCw%40mail.gmail.com.