Using VSTS Extension which calls GitVersion with /output buildserver /nofetch /updateassemblyinfo true since the update to 3.5.3 this stopped updating the AssemblyInfo files.
While, with the exact command line arguments for GitVersion, with Version 3.5.1 the following entry was output in the log, this is missing with 3.5.3:
2016-05-17T13:22:53.6468468Z Executing GenerateBuildLogOutput for 'VsoAgent'.