Charlotte,
Mainly the deinterlacing option is there because for a most compositing operations (roto, paint, keying, etc.) using interlaced footage would be a total nightmare, if not impossible; you always need to see the fine detail of the edges. One way of looking at it is that you are temporarily working on video footage deinterlaced in any compositing app, and then rendering back out in its native interlaced form if you need to. Rendering a Flipbook basically renders the viewer into RAM (similar to an After Effects preview thing), unless you choose Render Disk Flipbook which does create a disk QT file. Usually, you do all the final rendering in the FileOut node(s).
One thing you might check right away is to select your FileIn node and make sure you click on the “Auto” button to the far right of the timeRange Global parameters…this will automatically set your Global frame range of your footage, then click the little “house” icon at the bottom right of the Shake interface to set the frame range of your timeline (it sounds like you may just be viewing the first frame of your footage ’cause the time range is only set to “1” or something). If you have further problems, I’d suggest going over to the main Shake forum here at the Cow; those guys’ll figure it out.