The meaning of those flag

There isn't really any meaning to them, they're just substitutes for pixelation for when he curses on the show. They put the flag up so people can't read what he said by reading his lips and they also play voice-overs (like 'ohh-lala') as opposed to beeping out what he said :)

Well it shows the flag and has a voice over for that flag but the rainbow one beats me.

I FOUND IT !!!

When Ferguson (and guests) swear on the show, rather than seeing pixelization over his lips and hearing a bleep, the viewers will sometimes see a flag appear over his lips and hear a corresponding phrase, such as:

Austria: "Strudel", "Edelweiss", "Wienerschnitzel"
Australia: "Dingo ate my baby", "Crikey!", and "Crikey dingo!"
France: "Ooh la la!", "Croissant", "Baguette", and "Sacrebleu"
Gay flag.svg (Rainbow Flag): "Uh oh!", "Hmmm!", and "Ohhh!"
Germany: "Ausfahrt!", "Auf Wiedersehen", and "Achtung!"
Italy: "Tutsi fruitsi!" and "Wassacominago!" in a mock Italian accent in tribute to Chico Marx, with "Tutsi fruitsi" in reference to a sketch in the Marx Brothers film A Day at the Races
Nova Scotia: "Donair!"
Scotland: "Haggis", "Whiskey", "Breenge", "Shortbread", "Shut Yer Face!", "Dumbledore", "Bollocks".
Spain: "¡Ay, caramba!"
Sweden: "Girlwiththedragontattoo", "Lingonberry", "Smörgåsbord", and "Gravlax".

The bleeping effect is still used when Ferguson swears as one of his puppet characters, most notably Sid. Occasionally, the pixelization will still appear with silence in place of the usual censored beep.