Improper display of settings control on multi-site install

At the moment, all of my sites are using the default Garland theme as I rebuilt all of them into using Drupal 6 in September. Must add that I'm recovering from cancer treatments and can only work about 2-4 hours per day depending on how I feel. Getting custom themes up on my sites has a high priority, and I've been reading 2 different books on the subject for a while now. The designs side of things has been done for quite a while, it's doing the Drupal coding that I'm working on. (Have reached the total confusion stage as some of the things they say seem to conflict with each other!) Am coming to rely more and more on the wealth of info here and elsewhere to help me sort that out.

Hasn't helped that all of my content that contained JavaScript is not working now either. (Input Filter set to Full HTML Most are setup to open pop up windows.) Worked just fine in the Drupal 5 environment. Have posted a query on that a few days ago in the forum and am still stuck on that!

The sites do have different databases, and there is no sharing between them. (They are for 2 very different organizations.) If you mean the Help or Advanced Help modules, they are both enabled on both sites, although I do not have the included Advanced Help Example module enabled on the CEBUG site.

So far as I know, the CSS and JS settings within both sites are identical. That is, so far as I know, I've only made minor changes under the Performance setting. (Cache setting change to Normal on both sites.) Hummm, I see new settings in this area under Drupal 6 for optimization of both CSS and JavaScript. These are currently disabled on both sites.

Should mention that I did recently discovered that JavaScript inserted into content was no longer working after the rebuild into Drupal 6. For example in this page is a link for a JavaScript powered popup window that had worked fine when set to the Full HTML Input Filter within Drupal 5:
http://designworksinternet.com/web-safe-colors
Been going nuts trying to figure out why THAT's stopped working! (Stopped working before install of Better Formats.) Am considering rebuilding that into a Java Applet if that's what it takes to get that working again. (I'm a better programmer in Java than I am in JavaScript. But, as JavaScript has better support and is less intrusive, I'd prefer to stick to that for most things.)

The differences between the two sites. Here is a list of the modules enabled on CEBUG, where the problem is occurring that are NOT enabled on the other:

ACL 6.x-1.0
Advanced Forum 6.x-1.1
Calendar 6.x-2.2
Content Access 6.x-1.2
Flatcomments 6.x-2.0
User Badges 6.x-1.5
User Karma 6.x-1.0-beta1 (Just disabled this one on CEBUG site the other day as it does not appear to be working fully)

Here is a list of those modules enabled on the primary site (Design Works Internet) that are not used on CEBUG:

Media RSS 6.x-2.9
Addressbook 6.x-3.6
FileField 6.x-3.1
ImageAPI 6.x-1.6
ImageCache 6.x-2.0-beta10
ImageField 6.x-3.1
Invite 6.x-2.0-alpha1
Organic groups 6.x-2.0
Privatemsg 6.x-1.0-rc3
Thickbox 6.x-1.5
User Points 6.x-1.0
Views Slideshow 6.x-1.0-beta2

I have all modules installed as sites/all/modules simply so as to eliminate concern over different versions, and simplify - a bit - the task of doing updates. Secondary site is installed as /sites/cebug.org, which is how I thought you were to do that. Had set the permissions for the cebug.org folder to be 777, as mentioned in IMCE readme to resolve problems with permissions there. Can agree the better-formats-defaults-admin-form.tpl.php template file not being loaded is probably the root of the trouble, but WHY that is occurring is a puzzle.

Ordered yet another book on theming in hopes of making better progress there. The one I have here makes heavy use of the Zen theme, which is confusing the heck out of me. Not at all sure the code is really SEO ready either...