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As additional info, the Start-Transcript cmdlet is notorious for mssing output.
See for example #Issue10994 on the PowerShell repository.
I'm not sure if what you are seeing is caused by PowerCLI, I sooner suspect the type of output some PowerCLI modules produce when loaded might confuse the Start-TRanscript
Blog: lucd.info Twitter: @LucD22 Co-author PowerCLI Reference