Pager not displaying
I think I know what is going on. I've had this problem several times before.

The issue is that on some pages, multiple pagers may be in use. Which would explain why theme('pager'); wouldn't work.

I just had the same problem, and I got it working by doing this: 

theme('pager', array('element' =&gt; 1));


On my end, I wasn't displaying multiple pagers, but I think something else on the page must have been doing this, because the above code made it work! I hope this helps anyone else who encounters the same problem.