What makes it behaves that way? and how to solve it? Thanks in advance
The terminal colours affect any colours in the 16 or 256 colour palette. Most terminal emulators have a pretty standard 256 colour palette, but customize the bottom 16 colors to set the terminal colour scheme. Many vim colourschemes use these 16 colours, so will look very different depending on the terminal colour scheme. There are multiple methods to debug and fix this.
A good first step might be to work out how the 'launch from the search menu' and 'open in the terminal' methods of running neovim differ. Are they different terminals? etc.
- if using a custom vim colorscheme, follow the instructions on that. eg. a solarized colorscheme might ask you to set the terminal 16 colors to the solarized colours.
- if you can't or don't want to change the terminal colour scheme, look for a true colour (if your terminal supports it) or a 256 colour colorscheme for vim. this will give a standard look regardless of the terminal colour scheme.
- be careful reading older posts that talk about playing with vim options like
t_Coand friends; in newer vim versions and neovim these are rarely needed and mostly works out of the box. This can be a common gotcha. ;)