As a test, to se if your FCPX storylines project is in error or compressor settings may be of a negative affect, try the following.
step 1) just render all the storylines project in FCPX making sure that all and everything has rendered in FCPX , then export "share master" to make a self contained qt movie using the same codec you have in the FCPX project. This will be basically copy operation from FCPX and should involv minimal to no rendering time addition.
Step 2) on completion of step 1. open up compressor and stop Qmaster if its running. (You can restart it later). In step 6 u will submit this master using the same host resources that FCPX would have used on you FCPX host....
Step 3) add the master object from step 1 into compressor GUI
Step 4$ check the inspector in compressor for that batch job that "frame controls are OFF" and set multipass to off
Step 5) submit the job to "this computer" and see if transcode runs to completion.
This will ascertain if it doesn't run that the qt components used by compressor.app et al ad having or not having trouble with the master clip.
Yes it will take longer than using a cluster but this is only a test.
If this works ok, the using the same setting, try with your cluster. (Submit to cluster)
Post your results for others to see.