SSIS package fails intermittently with: Unsafe assembly 'microsoft.sqlserver.integrationservices.server, version=11.0.0.0
This has now run successfully for ~1.5 weeks. The more I think about it I believe that the ssis error (posted in title) was a side effect, and was the result of the timeout caused by the dataload connection.

I can't prove or disprove if installing SP3 had any effect at all.

In my opinion the comment from @TheGameiswar is the best indicator pointing to root cause.