We are seeing the same issue with MultibranchPipeline jobs with Windows Server 2012 slaves. Rolling back a number of Pipeline/Workflow plugins solved the issue for us. We were not able to identify exactly which of the pipeline related plugins introduced this issue, but since they are very interdependent it would not help us much anyway.
We are also stuck with an old version of Blue Ocean since it requires a newer version of the Pipeline plugin which would introduce this issue again.
Below is the combination of Pipeline related plugins which has not yet introduce these error messages for us (... java.io.IOException: Remote call on Channel ...):
pipeline-build-step:2.4
pipeline-github-lib:1.0
pipeline-graph-analysis:1.3
pipeline-input-step:2.5
pipeline-milestone-step:1.3
pipeline-model-api:1.0.1
pipeline-model-declarative-agent:1.0.1
pipeline-model-definition:1.0.1
pipeline-multibranch-defaults:1.1
pipeline-rest-api:2.4
pipeline-stage-step:2.2
plain-credentials:1.4
pipeline-stage-tags-metadata:1.0.1
pipeline-stage-view:2.4
workflow-aggregator:2.5
workflow-api:2.10
workflow-basic-steps:2.4
workflow-cps:2.26
workflow-cps-global-lib:2.6
workflow-durable-task-step:2.8
workflow-job:2.10
workflow-multibranch:2.12
workflow-remote-loader:1.4
workflow-scm-step:2.3
workflow-step-api:2.9
workflow-support:2.12
After I figured out how to turn on more logging messages, I got this: