To what format are you encoding your loop and what program are you using to encode ??
Asking this coz if you're on AE CS4 or below, you would be encoding your loops in another program, just like i use TMPGEncXpress4 to encode my .AVI files to .MPEG-2
Also I would suggest you that most of the footage dreams like the ones you've recorded from your camera loop better if you use the following method-
After Effects Looping Tutorial
For the animations created in After Effects, you can use the settings to set the loop time, almost all plugins too have the option to set loop time.
Anyways, if you do not succeed with any of the above or find them tough, then simply do the following-
Split your video into 2 halfs, drag the 2nd to the end of the Comp, holding down shift, make sure you maintain a little overlapping between both the layers,click on the top layer, hit T to bring up the Opacity of the layer, click the stop watch, move a few frames ahead just where the 2nd layer begins, here just bring the opacity down to zero, this will crossfade and your output video will loop seamlessly
For any further help, you can sure pm me anytime,
Amitsaran.