That thread has been updated again and Toni has come up with a new vsync method (no need to "calibrate" your refresh rate).
Works great and will be included in the next beta I believe
Also, you're using a 1080p tv like me I think? I've recently switched to using no filter at all and no aspect correction. Just Horizontal Size to 2x, and Vertical Size to 4x. This ensures that there are no scaling artifacts at all for a very, very clear picture. The amiga screen fits quite nicely on a 1080p TV. Not all games will fill the screen vertically of course (same as on a real Amiga) but the "automatic center" option can be quite nice in these cases.
Scanlines & bilinear can still be turned on if that's your thing