Why are some variables and comments in my IPython notebook red?

This is because the indentation is screwed up.
For consistency the codemirror parser will make a red line if it’s not indented 4 spaces (or if it’s indented with tabs, depending on codemirror version). The parser has some edge case that indeed highlight only a few of theses lines in red, I won’t go into details, but if you indent 4 spaces it will work.

You can either:

• select the block of code and press tab
• use alt–click'n'drag vertically to place multiple cursors in front of your code, and press space enough time to make the correct indent 4 space.

Setting the indent to 2 is possible, but complex and not recommended. 4 space is the python norm.