Johnny, in the past few weeks I've learned that 1.1 had a flaw in my thought process as it relates to the extra fields. Last night I posted a fix and an update for the 1.8 release.
One of the problems I had was that if a type of ad had different extra fields for various categories, we wouldn't know which ones to pick up because we didnt ask them which category to upload to first.
The latest build is a three step process (if you have multi ad types, otherwise two):
1. pick your ad type (this is skipped if you only have one ad type)
2. pick you category
3. fill out your ad
If you use different extra fields within the same ad type, you're going to need to get the latest update so your users are always prompted for the same ad information.
The issue with submiting ads from the non-category areas was also resolved by forcing people to pick an ad type.
The change we offered from before which changed the query to get extra fields using the template number should cause you to pick up the proper fields if they are always the same for an ad type; you'll need to make sure this is the care (type printing out the query in uploadproduct.php (print $query

to see what you are getting and then execute the query in a MySQL to see what results you get.
I seem to recall you were using 1.1 and not wanting to upgrade; so fixing it to the 1.8 standards would require you to make the mods yourself.