Item-specific template variables will only work in product-specific Message (HTML) fields; they will not work in the Common Thank-you Page HTML field because that field is not associated with any particular product. Your E-junkie-generated thank-you pages will include both your Common Thank-you Page HTML at the bottom of the page and the Message (HTML) for each item ordered.
This help page lists which template variables will work in which fields, and at the end of the page you can see an example demonstrating which customization fields get inserted where:
http://www.e-junkie.com/ej/help.custom.thankyou-page.htm
If you need to use some Order Specific variables that aren't supported for product-specific Message (HTML) fields, you can split up your tracking javascript to declare JS vars where needed -- e.g., if your tracking code needs to have something like this:
<script type="text/javascript">
var price='[%sale_price%]';
var item='[%item_name%]';
var total='[%gross%]';
</script>
...you could put this part in your product's Message (HTML) field:
<script type="text/javascript">
var price='[%sale_price%]';
var item='[%item_name%]';
</script>
...and put this in your Common Thank-you Page HTML field:
<script type="text/javascript">
var total='[%gross%]';
</script>
One issue with this is that orders for multiple items would have the same item-specific vars declared multiple times, which can be a problem if your tracking code doesn't provide a way to distinguish vars for one item from another. In this case you may need to use our Buy Now buttons, which bypass our cart and take buyers directly to instant checkout for just one item at a time:
http://www.e-junkie.com/ej/help.buttons.buy-now.htm
Finally, bear in mind the caveats about thank-you page visits explained here:
http://www.e-junkie.com/ej/faq.tracking.conversions.htm
Download buyers would need to visit their E-junkie thank-you page at some point to claim their download, but if you're selling tangible goods or services rather than downloads, see the tips here to have buyers auto-redirected to your E-junkie thank-you page after checkout:
http://www.e-junkie.com/ej/tips.tracking.conversions.htm