I'm not quite sure what to do here. This is code for a Simon style game, and while currently pretty functional (and with GUI pending) I can't get the entire sequence to flush. It flushes the most recent output only. I've tried flushall and multiple << flush but these simply don't work.
Flush in this case just means that everything that you have written to cout is made visible. To overwrite the sequence that you have printed I think you will have to print the '\010' char (or '\b') as many times as the number of colours in the sequence and print equally many dots.
If you're trying to clear the screen like Peter87 suggests then since you're already including windows.h I can assume you have no trouble including wincon.h as well. Here is some code to read over:
EDIT: This is some copy pasta from a console "game" I was playing around with about a year ago. In my version I made 'hOut' a global variable since it was needed elsewhere and it didn't make sense to keep grabbing it and\or passing it around every time I wanted to clear the screen or what ever, that's why it isn't closed as would normally be the case.