I got pagination to work by modifying the setTreeGrid function. I commented out the following line:

$t.p.pgbuttons = false;$t.p.pginput = false;

The buttons then appeared and the requests were going back to the server to request the information. Now for this I was loading the entire tree to a local variable then using setJSONData to load the data into the tree. It functions the way I would expect it to.