Why do I get a Rattling noise from transmission when i release the clutch.

Have you had the throw out bearing and the flywheel checked yet? Typically, that kind of rattle can be a sign of a component on its way out. With the engine cold (first starting and short trips) the vehicle will not get hot enough for components to expand and shift (not as loud of a rattle). In most circumstances, the shop that did the work should have you covered by a warranty, if you genuinely think that there is a problem, take it back to them and have them check it again and if they find nothing, make sure they put it in writing (your concern, diagnostics, and findings), if your still not happy with the findings, have a second opinion done, it might cost a diagnostics charge, but it could save you a lot of time and money (and possibly a break down!) if the rebuild is under warranty from your primary shop!