Google-sheets – Why is a conditional formatting range mis-applying some cells

In your spreadsheet, go to tools, click script editor, and create a blank script. Replace any text inside the script with this function.

function paintRed() {

  // Gets the entire workbook
  var ss = SpreadsheetApp.getActiveSpreadsheet();
  // Gets the sheet you are concerned with
  // Change Sheet1 to the name of your sheet
  var sheet = ss.getSheetByName("Sheet1");

  // First 6 cells of the first row
  // Change to whatever you like
  var rangeToPaint = sheet.getRange("A1:F1"); 

  // Gets the number of the last row in the sheet 
  // that has anything in it
  var lastRow = ss.getLastRow();

  // If the sheet is blank, set the first 6 cells
  // in the first row to white and end the function
  if (lastRow < 1)
  {
    rangeToPaint.setBackground("white");
    return;
  }

  // Gets column A and column C
  var rangeColumnOne = sheet.getRange("A1:A"+lastRow.toString());
  var rangeColumnTwo = sheet.getRange("C1:C"+lastRow.toString());

  // Gets the length of column A and C
  var column1Length = rangeColumnOne.getValues().toString().replace(/,/g,"").length;
  var column2Length = rangeColumnTwo.getValues().toString().replace(/,/g,"").length;

  // If column A is blank or column C is not blank,
  // set the first 6 cells to white and stop the
  // function
  if ( column1Length < 1 || column2Length > 1 )
  {
    rangeToPaint.setBackground("white");
    return;
  }

  // Otherwise, paint the first 6 cells red
  rangeToPaint.setBackground("red");

}

You will need to change Sheet1 to whatever the name of your sheet is. Then, while still in the script editor, click resources, 'current project triggers.'

Add a new trigger with 'Run' set to paintRed and Events set to 'From spreadsheet' 'On edit.'

You should be good to go.

Link to spreadsheet you can copy to your drive, then play with - https://docs.google.com/spreadsheet/ccc?key=0Ar6b2EOADTG7dGJOM0lEalhjd3pNOHNRNnBDOV8xRnc&usp=sharing

Something seems to be off with the conditional formatting. One solution, anyway, as Vidar suggested, is to use Custom formula is instead of Greater than in the dropdown. Use the formula =B5>$B$3 with your range.