Input indicator (or "language bar" in case of Windows 7) disappears when a published app gets in focus:
The issue is caused by interaction of RAS and Microsoft ActiveX component.
Engineering team is aware of the issue and is working to address it.
There are two possible workaround at this moment:
Enable option "Use the desktop language bar when it's available" on the RD session host.
To do it, please Proceed to Control Panel → Clock, Language, and Region → Language → Advanced settings and tick the checkbox:
Please take into account that this setting is applied per user. Once you enable it, this icon will appear in the system tray when a published app gets in focus:
The second possible workaround is to enable utilization of RemoteApps for RAS. This option is applied to the whole RD Session Host.
To enable it, please launch RAS Console and proceed to Farm → RD Session Hosts, open the properties of the desired RD Session Host, switch to "Agent Settings" tab, clear the checkbox "Inherit default settings" and mark the checkbox "Use RemoteApp if available":
Users will need to log off their current sessions to apply the changes.
Please take into account that this feature will disable "Drag and drop" for Windows users.