The caret (name of a text cursor) is blinking always with the opposite color of the current background color. For example if the background color is yellow (active line) with RGB value #FFFF00 the caret is blinking with color blue with RGB value #0000FF.
The background color can be
- the background color of plain text if active line/column highlighting is not enabled, see Manage Themes - Editor - Plain Text,
- the background color of active line/column highlighting if either active line highlighting or active column highlighting or both are enabled, see Manage Themes - Editor - Active Column and Active Line,
- the background color of a read-only file if active line/column highlighting is not enabled, see Manage Themes - Editor - Read Only Background,
- the background color configured for a color group in a syntax highlighted file different to normal background color, see Manage Themes - Syntax - Language - Color Group,
- the background color set for bookmarks, or XML/HTML tag highlighting, or brace highlighting depending on which of those features is enabled, content of active file and position of the caret.
So if you see the caret blinking with a color not being well for seeing it, the appropriate background color is not right configured for the theme.