I believe what might happened is your SOLIDWORKS resources are overloaded - so it reached the limit. Basically if you would try to open this model and activate/save each configuration manually you will have similar issue.
We have fixed that problem by implementing another option to 'Treat each configuration as an individual item' while processing multiple configurations
This would allow to consider configuration as a file and respect this option:
Which would allow to free the resources after X amount of configurations. Furthermore in case of the crash of SOLIDWORKS it will continue on the last processed configuration.
This functionality will be released in #TASK 2.0 which is just few weeks away.