One thing to consider as a workaround to this is to use php5-fpm for per-user PHP, running a daemon per user. This has the additional benefit of being able to limit each user's memory usage individually. You can then switch to apache worker, which I'm sure does not have this issue. This should also be quite a bit more memory efficient as static files will be served from the apache threads rather than all 1000+ processes.
One thing to consider as a workaround to this is to use php5-fpm for per-user PHP, running a daemon per user. This has the additional benefit of being able to limit each user's memory usage individually. You can then switch to apache worker, which I'm sure does not have this issue. This should also be quite a bit more memory efficient as static files will be served from the apache threads rather than all 1000+ processes.