Couple questions… what version of Magento 1.6 did you have? (18.104.22.168, 22.214.171.124, 126.96.36.199, etc)
Which method did you use to upgrade your site? Did you:
A) Use the mage script to run a site update on all files in the site
B) Copy the new site files on top of the old ones and run install.php
or C) Create a fresh installation and migrate the data into the new install, subsequently using the Database Repair tool to fix inconsistencies
... if you’re having trouble with the migration, I suggest you start with A, then do B, and if all else fails, try C.
Please try to remember to keep a solid backup separately of your working site from 1.6.
Try to do all of this stuff in a “validation environment” (a test server) before doing it on the live server.
Believe me, I know what these headaches can be like! I will be a very happy camper when all of my idiosyncratic tweaks are working properly in v1.7 =)