I was able to create a scenario to reproduce this. Maybe this will help find a solution.
In ZendEnablerConf.xml set the connection timeout to 5 seconds and the request timeout to 10 seconds (<Timeouts connectionTimeout="5" requestTimeout="10" />). Set it to only startup 1 process (<ProcessCount start="1" extra="1"/>). In the php.ini set the execution time to 30 seconds.
create a php script that does the following:
1. sleep(8) // wait for 8 seconds
2. create a soap call (or MSSQL db call) that will take longer than 2 seconds.
3. open a browser and reload your test page 5-10 times quickly, not waiting for them to complete/timeout.
In our case, this represents a valid production scenario. We have SOAP requests that can take 2-3 minutes at times so we use php's set_time_limit() to increase the timeout on the fly before we make the SOAP request. I believe this is conflicting with Zend Enabler's request timeout setting, which causes the timeout and the apache php process to hang up.