Following comes from Deepak Mittal, Senior Developer Support Engineer.
If you are using custom assembly check-in operation and lab build in the same build, you may notice that the build will hang, though custom check-in operation will succeed.
If you will review the build log, it will most probably show the last action as “waiting for workflow capability to be ready”. There will be no error message or event logs other than that in the build log
This is by-design. Reason is, when the custom check-in operation happens it will send the controller into offline status, but the lab build will look for the controller to be in online status.
There are two suggestions which you can look for to work around the issue:
1. Create a separate branch in source control for custom assembly check-in operation and merge it with your main branch later.
2. Do not perform both operations simultaneously.