Welcome to the Forum.
I think you will find this a generic message to do with the
registry.
"80070002 - The system cannot find the file specified."
What I believe is happening, based on your post, is that in
some cases, depending on the speed of the machine, the
unregister/register of the file is not quick enough to complete
before the file is looked for. By the time you have dismissed the
dialogue, the file has been properly registered and the
installation completes normally.
This happens in many applications. If you Google search on
the error, you will see hundreds of entries relating to this
message across all applications.
Sorry, I don't know of a way of stopping it completely, but
as you say it is harmless.
Brian