Moving it to CM users list as this is more of a CM+CDH installation issue.
So original install was using Parcel? I presume that now everything is
running using packages, but can you please confirm. You can look at full
path of command line of HDFS/MR process to figure that out. You can also
look at cloudera agent log (/var/log/cloudera-scm-agent) on any worker node
to see if there is any error reported there. Agent is the one that reports
CDH version to the server and may print diagnostic message in the log if it
can't find that.
What is going on here is that agent process isn't able to read the file
(maybe its looking at wrong location because of package/parcel switch) and
thus not able to report it to the CM server.