I've upgraded my site (to 1.4.1) into a temporary directory in my current site. I've copied over my only theme (Professional, I think slightly modified) without any changes into my layouts folder. The colors and everything are correct, but the text size is different, the spacing is off, and my copyright message at the bottom is back to being the default.

The text size and spacing I would think would be controlled by the style.css file in my theme, but the two files are identical.

Original site
Upgraded site

I know, I know, read the manual, but everything seems to suggest that the style is controlled by the theme, and the two theme folders are identical.

Hmmm.. and the other problem is that by just copying the entire theme directory, I seem to have made the theme non-1.4.1-compliant. For example, my registration page has only one email field, and so I get an error when I try to register as a new user. I've now found and copied over the new theme's code for registration. However, what is the standard way to keep your theme after upgrading? Should I have re-installed Professional and then gone back in and made changes..? Or keep my old one, and try to work out what's changed?

You cannot do that. There are many changes between 1.4.1's professional theme and prior professional theme files that are necessary for 1.4.1 to work -- new template variables, dropped template vars, etc. What you should do is find the files your modified and apply "equivalent" changes to 1.4.1.

The same thing will happen when 1.5 is released in a couple/few months. Every new version invalidates some part of every theme

Wow. That's going to be way more annoying than when I discovered that you can't simply copy over all the lib-custom.php functions because all of a sudden all the function names had changed...

Now, is there some way to download an old version of the Professional theme, and then do some kind of diff on the entire folder, so I can see where all my changes are? I mean, there must be close to 200 files in there.

It's really dumb to make dramatic changes to the basic Professional stylesheet. I can understand changing variables and other coding changes, but changing the way fonts operate? Dumb. Just really dumb. We upgraded our busy Geeklog site this weekend and I'm really irritated that minor tweaks I made in blocks to make some links bolder don't function with the new style sheet. Given that Geeklog has no theme editor, it's already hard enough as it is to make the basic Professional style sheet user-friendly.

I really like Geeklog, but breaking the basic stylesheet with every upgrade is just going to send me over to the Drupal camp.

Best practice with Geeklog is to copy the shipped professional theme to another name "default" and set $_CONF['theme'] to 'default'. Then when you upgrade, move everyone to 'professional' so the site works and worry about getting it to look right later. Annoying, yes. And probably "too late now". But that's how it goes.

Do you think it is better there? I remember dramatic changes in the layout and even complete changes in the technology. They had templates and special template engines.

The changes you do in a Geeklog theme are mostly only with a few files like 3-10. It is relatively easy to keep track of them e.g. they have a different date on the server than the unchaned files.