Sorry, but possession of an AE template is no guarantee of AE success; their makers assume you have AE knowledge.
Since you seem to lack it, we'll need a lot more information:
and don't forget to include screen shots of the timeline and the project windows. I know you tried, but there isn't enough for a good diagnosis.
What kind of image are you trying to add and how do you know it has a transparent background. If there was truly an alpha channel and the value of the transparent part was 0 then it would be transparent. If the value is anything else then there is partial transparency. Check the info palette:
Here's the info palette when the cursor is over an area of partial transparency
This is what it looks like when you are over an area of complete transparency:
The second shot if the info panel is what a comp should look like with only your logo file in the project and the cursor over the transparent areas.
For us to tell what's going on make sure that you have your problem file selected in the project panel so we can see the properties, then select the problem layer in the timeline and press the U key twice to reveal all changed properties. If the problem layer is a pre-comp then you'll need to drill down to the location of the original footage that is giving you problems. Without this info I can only assume that your logo file does not truly have a transparent background. If it does, then there's something wrong with the way the file has been added to the timeline.
i actually created a logo from scratch in photoshop with alpha channel present.
thanks for your replies but it was a roughen edges effect that messed up the logo.
this thread can be locked or whatever