I'm talking about basic ML functionality on HDMI - like zebras aligned with the image etc.
I haven't had a chance to fill out the survey yet, but here's the only issue I've had on my last 4 full day shoots. I've been using alpha one almost exclusive via HDMI with my SmalHD DP6. Everything I've tested works great; audio meters, fast zebras, focus assist, histogram, vectrascope, an even the manually enabled "Not recording" warning. Here'a what I've had enabled on my long day shoots: "not recording" warning, audio meters, histogram (with gradual warning), and LumaFast Zebras over 99%. The only time I have a problem is when I leave the camera on but power cycle my monitor. When the monitor comes back up, the 16x9 crop bars scale down a bit, slightly covering what should be the proper visible area and revealing part of what's actually not recording.
See this photo showing what I'm saying.

Other than that, I've had no alignment issues with any of the features (zebras, focus assist, etc).
Edit: I should add that to get around this, I simply reload the ML firmware.