have you edited any of the loops???
Are these stock loops that come with Acid???
If so.....I have never had any stock loops that weren't smooth but regardless you can right click on the offending loop in the Acid explorer and open your editor of choice (perhaps Soundforge wich should come with the Acid disk) and clean them up.
I usually enable "loop mode" in SF and then drag the edges of the selection region until the timing is right.....then just drag the selected region to a new window or the blank workspace.
Also....make sure to enable the "snap to zero crossing" feature in the Sound Forge OPTIONS>PREFERENCES>EDITING drop down.
This should eliminate any clicking....it ensures that any edit points automatically move to the nearest "zero crossing", or null point in the wave so that since the beginning and end edit points are snapped to zero points, there should be a perfectly smooth transition as the loop......loops.
Hope this helps.
-mike