Unfortunately as of yet the linux receivers don't seem to autodetect 3D content and spit the trigger signal to the TV despite the ''auto'' option.
I get around this on Vu+ Duo by enabling a macro on my Harmony One that works quite well
1st off enable the 3D OSD in the extensions Menu, with off as default.
I have 2 macros programmed, 1 for 3D on and 1 for 3D off.
EditI'm assuming the image used on the receiver is Vix in this macro
My macro is as follows, 3D on = Blue Button> 1(Or whichever number 3D OSD is in Blue Button Menu)>Right(Enables Side by Side)>Green.....
With this Macro my TV(LG 55LW550) then Autodetcts and switches to 3D mode.
To resume normal 2D my Macro =Blue button >1(Or whichever number 3D OSD is in Blue Button Menu)>Left>Green.
This switches the Vu back to 2D mode and again my TV autodetects 2D.
As I have both these macros programmed to single keys on my remote it saves an awful lot of faffing about with regards to using my TV remote or switching modes on my Harmony to enable 3D