Added a Jquery slider and header no longer rotates

Hi,
I have added a slider to the localhost version of my website for showing smaller sets of photos within the body of each static page.

To get the slider working I added the latest Jquery in a file named jquery-1.4.2.js to the Wordpress folder, as well as the slider file which I named as cyclelite.1.0.js.
The slider is a jquery operated js slider and does not load via the normal wordpress plugin route.

I add the image names in each static page so the slider can use the images that reflect the content of each page when each page is viewed. i.e. different images for each page.

Should I have put the operating files somewhere else? Although the slider is working fine, unfortunately the header which is operated by Atahualpa has stopped automatically rotating. The images only change if I refresh the page. If I remove the slider then the header starts rotating again.

Does the header use a different form of Jquery for rotating and fading which may be causing the conflict between the two?

I am using:
Atahualpa 3.5.2
Wordpress 3.0
Jquery 1.4.2

Can anybody help or do I just have to choose between whether I want the header or the slider to work?