Saving Configuration for all settings

[Selur]

X264>Base>Configuration>choosing, applying “H264 Hybrid Default” (For some reason need to click Configuration Apply arrow twice in order to stop data changing in the Command Line window. After second click it was changed).

Should I click once or need to click twice?

No clue why it requires 2 clicks for you, works on my system on the first click.

X264>Frames>Max Number of Reference Frames – setting slider to 5 (Or using Slow Preset)

If Ref Frames set to 3, Command Line shows: ref 3
If Ref Frames set to 4, Command Line shows: ref 4
If Ref Frames set to 5, Command Line does not show ref xx anymore, why?

Because that is the default values (of either the 'medium' or the preset set by '--preset XX' are hidden.
If you want to see a command line with no hidden settings disable 'x264->Misc->Main->Adjustments->Minimize command line'

Just an idea, that Preset and Tune should be as separate “Presets” Section/Box, not included in to Restrictions Section.

I'll think about it.

If encoding timing is not a big issue for me, what preset is recommended for VHS, DV avi captures form camcorders?

Encoding settings don't matter that much, better learn how to properly filter your content. ('slow' and 'slower' are the only profiles I usually use as a base for my settings)

Cu Selur