Two ideas:

You could check if the webserver process has the same ulimits as the shell you ran ulimit from.  For this, just have a CGI script run ulimit and return its output.

As you get the "out of memory" after the last instruction of the worker script, it could be that some cleanup code in destructors, END blocks, or the Perl interpreter itself (I suppose the worker is a Perl script, too), is using more memory than available at the time.  So you could try POSIX::_exit to exit the process immediately, bypassing any cleanup.