There is a limit to how high standings will go. If you're playing with humans, you already start out at 10.00 standing. You can use envoy ships to bump up your standing by 1.50 for each planet (you only need one envoy ship on a planet to maintain this rating, but many envoy ships can be sent to a single planet to quickly build it up). Also, I'm not 100% sure about this, but giving resources only gives up to 1.00 standing increase (which can further increased by doing the appropriate research to 3.00 standing increase).

Sounds like you have one envoy ship at one of their planets and you are sending tons of resources for the other 3.00 (I'm guessing you did all the research for that in the diplomacy tree). You'll need to send more envoy ships to your ally's planets (and if he only has one planet, then, well, there's not much you can do beyond helping him colonize further).

EDIT: Oh yeah, that's only if you're playing vs. humans. Against the AI it's pretty tough to get the standings up there with envoy ships and diplomacy reserach alone; you'll also need to do the missions they offer you!