The reason I asked is that I worked on this  bug
<http://wixtoolset.org/issues/4592/>  , for Wix 3.10, which is not the same
scenario that you observed, but may be related.  The pull request was
accepted last week, and I don't know if there has been a build of wix 3.10
with this change yet.

I also had issues with a tray app, particularly when it was started by a
service.  Our product includes both desktop clients and services, any of
which may launch the tray app, so there may be multiple instances of the
tray app running.  Our tray app originally did not have any message pump
(which is needed for RestartManager or ClseApplication) so the dev added the
message pump in a hidden window.  The wix implementation prior to
integrating 4592 in 3.10 is that when trying to register a process name (the
name of the tray app) with RestartManager, it tries to open each instance of
the process.  When the tray app was launched by the service, it is running
in a different user context than the msi thread related to RestartManager
CAs and the attempt to open the process object failed causing the whole
setup to fail and rollback.

The wix-dev folks advised me, and I implemented a change to 'try' and add a
permission to the CA thread to allow a process in another user's context to
be opened, however if the installer is not elevated, then we cannot do that. 
So in that case the new implementation is to skip registering that instance
of that named process, post a warning in the log (not error), and continue
the setup.  In those cases my mba detects if a reboot is needed and prompts
for a reboot.

I understand the RestartManager in general tries to avoid reboots, but does
not guarantee that it won't still signal for a reboot.  So the change was to
treat a failure to register a named process as a 'we tried', but do not
fail.  It sounds like this is not the situation you have, but maybe this
information will be helpful in some way.

Phill



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