What cover do yo have, Ella? Is it the standard 'travelling' cover that is supplied with all Dandys that has leaked, or do you mean a secondary cover you have put over the top?
The brown cover that came with our Dandy has a little nick on one corner but thankfully has never leaked in. I have treated her to a Kampa all-over breathable cover a few weeks ago - and I mean 'all-over' - I ordered a size too large by accident so it covers everything including the gas locker & tyres!
I thought I would keep it instead of having the bother of exchanging, and anyway (I reasoned) covering the tyres can't be a bad thing as they are then protected from UV etc.
I think if our Dandy's travelling cover leaked I would fork out for a replacement or try to get it mended, although I believe they are not cheap. They are so crucial, though, as if water gets in it can do untold damage.