Hey fosex,
I'm going to number your questions so make this easier 
1. (2 transports in a fleet): This should work. Is anyone else having a problem with this? Make sure you have over 10 logistic points (even though I know you said you had them, but just triple checking).
2. (Attack option while trading): I beleive the attack option will only appear if the race your trading with is at "less than friendly" relations with other civs.
3. (selection designs to appear in other games): No, you have to obsolete on a per-game basis.
4. (clicking on buttons for other ships): Yes, these aren't doing anything. We should probably hide them or something, so players dont feel like they're in control of alien vessels.
5. (cant get info on stacked fleets): interface issue...will put on our list
6. (haywire screens): Unfortunatly it sounds like you're playing on a card that dosent support DirectX (which is part of the GC2 requirements). These things happen when the card only supports OpenGL. We'll try and look into a fix, but unless they have new drivers that fix the issue, it'll jsut have to be haywire for the time being 