I have thickbox working on my thumbnail image (as well as detailed). I moved the thumbnail code to the thickbox template in product.tpl
move the thumbnail code from product.tpl to thickbox_productpage.tpl (or whatever you call your thickbox template). I am not using the latest thickbox -- but the technique should work.
Code:
{include file="product_thumbnail.tpl" productid=$product.productid image_x=$product.image_x image_y=$product.image_y product=$product.product tmbn_url=$product.tmbn_url id="product_thumbnail" type="P"}
yes?