Are you using Chrome Remote Desktop to access the console desktop (ie, what you'd see if you were sitting in front of the computer)? This is not something we officially support--normally, CRD on Linux creates a separate, virtual desktop so I wouldn't expect you'd see any windows from either monitor when you connect to a Linux host.

If I've misunderstood your problem, perhaps a screenshot would help. Please be aware that this is a public bug tracker, so be careful to exclude anything sensitive if you attach a screenshot.

No I am trying to access Gnome desktop not console desktop. When I start Chrome Remote desktop I am able to login and see windows which were opened in primary monitor.

Lets assume, In your host machine (Ubuntu) you launched any application  and you moved it to display in second monitor. Now from your Mac machine you started Chrome remote desktop and try to launch same application, it is not showing (it might be launched but not visible). If you check the processes (using 'ps -A') you will see it as running

We chatted about this off-line. It turns out that the problem only affects Chrome and is caused by explicitly overriding --user-data-dir on the command-line in both the console and virtual sessions. Since this overrides the CHROME_USER_DATA_DIR env variable we set in the virtual session, when this command is run in either session it just opens a new window in whichever session launched Chrome first (in this case, the console session). The fact that Chrome was running on the secondary monitor was a red herring.

Since Chrome can't handle running on multiple DISPLAYs with the same profile, this is WAI.