Why are you using such an old release?
The most likely cause of the trouble is that the XML parser is fetching DTDs or similar files from the W3C server. In the last couple of years W3C has started to discourage this practice by artifically delaying the response from the server; Saxon has responded by including local copies of the files within the JAR. But to take advantage of this you will need a recent release.
Incidentally, you might like to try Saxon/C as a better way of invoking Saxon from PHP.