That's because then you are sending different commands - the receiver knows that "1" "2" must be two separate keypresses, whereas with "1" "1" it thinks both of the IR bursts are part of a single, longer press of "1" unless there's a long enough pause between them.
Some remote control protocols work around this problem with something called a "toggle bit", which means that repeating commands actually send a different code with each keypress, and you don't need the delay. Apparently the Virgin box doesn't do that.