ENBSeries

For some reason version 229 makes things flicker on interiors, walls go missing, objects vanish and i get the old blue level bug we had during the skyrim launch where whole dungeons appear missing.
I also get strange horizontal line blinking like a broken TFT panel and ghosting (even the mouse cursor on the main menu seems to ghost but this does not always happen).

146 is fine (with same config and presets)

Any idea what might be causing this ?

Running with 2 nvidia 670 cards in SLI.

Try turning off MultiSample in Skyrimprefs.
Try removing any earlier-edited ENB files and replacing them.
Try re-installing Skyrim if you're experiencing missing objects.