Something I don't understand with Ripple:
When I log in my Ripple wallet I have 44,000 XRP. But when I try to make a deposit with Ripple at Bitstamp or Justcoin my balance show only 1,000 XRP and I can only deposit this 1,000 XRP. Why ?
I'm not sure I understood your question but could it be the trust line?
It could very well be that because I have no idea what is the trust line. What it is ?
And what should I do to be able to deposit my 44,000 XRP at Bitstamp ?
XRP doesn't require any trust lines. That's one of the things that makes it special within the network. Bitstamp doesn't allow XRP deposits and honestly why would you? Storing your XRP in your Ripple wallet is how you store it, without counter-party risk. If you want to sell or buy XRP, you simply need go to the trade section of the client and change your issuer to Bitstamp or whomever you choose, for the specific currency pairs you're interested in. That will give you access to their orderbook.