Animated Gif image with transparent background

SirChick

I am having issues with making my animated gif image.

Basically, I have a logo with some areas of the image transparent for a website.

What i then did was animate lightning effects to it for practice. Now when i uploaded the non animated version to my website it looked fine, but when i uploaded my animated version it went horrendous in terms of a particular layer. The layer is the second one in the list:

1.Background layer
2.rain layer (non animated rain, just a brush preset i made)
3.lightning layer (the animated layer)

I have attatched two images to show you what happened between the changes. The blue cloudy background is the website's background not the actual image so the image background is transparent even though it doesn't quite look like it is, if you get me ?

Let me know if i have missed out any important infomation that you may need to know to aide me in fixing my mistake.

Thankyou in advanced.