I'll take a look as this was very likely caused by a change I made.

Please try using this snapshot:

  http://snaps.php.net/php5.4-latest.tar.gz
 
For Windows:

  http://windows.php.net/snapshots/

I expected that change to resolve the issue, but it did not. It's now skipping the 
call to _php_libxml_external_entity_loader but the stack trace is otherwise the 
same.

Ah. Then this was caused by d8bddb9. xmlParserInputBufferCreateFilenameDefault() et al. are called purposely on MINIT (before: RINIT) and your extension is loading after libxml.

This can be fixed in two ways. We can either call the original handler from the custom handler if the modules are not initialized, like we now do on _php_libxml_pre_ext_ent_loader, or we can try to set the custom handlers lazily and once on RINIT (not complicated since we don't have to worry about threaded SAPIs, which always do initialization on every RINIT).

Both options are ok for MINIT. The first option has the advantage it has predictable behavior on RINIT (whether your extension is request activated before or after the libxml ext, you don't get the custom handlers), but it may have BC impact (some modules may have been relying on the custom handlers and on being loaded after libxml -- which I think they can guarantee if the declare a dependency on the libxml module).

I didn't realize 5.1 added module dependency checks so I updated the source to 
include them (https://gist.github.com/2896852 ).

It seems to me that all the custom handlers (php_libxml_error_handler, 
php_libxml_input_buffer_create_filename, 
php_libxml_output_buffer_create_filename) should check for module activation 
same as _php_libxml_pre_ext_ent_loader. Of course, setting the custom handlers 
lazily in the first request would prevent the need for all those checks. As for 
BC, how could this be working for any other extension?

BTW, do you know exactly what is causing the root issue in the streams IO 
functions and why zend_register_resource segfaults when updating the hash table? 
Are streams not initialized until after module activation?