Just wanted to give you all an update, and help anyone who reads this who might be having similar problems.
rfischmann and ewizac both contacted me through the WP-SpamFree Support form, and through a little troubleshooting, we were able to figure everything out.
As I suspected, in both cases there was a conflicting plugin, so WP-SpamFree wasn't malfunctioning at all.
The plugins causing the problems were AskApache Password Protect in one case and WP-OpenID in the other. Both of these are coded in such a way that they can hinder the performance of other plugins. For more info, please see the Known Plugin Conflicts list.
I'll be looking at how to possibly bridge the conflicts and that includes contacting the plugin authors and letting them know of the conflict. If there are any workarounds I can add to WP-SpamFree, I'll work on that as well.
I work hard to make sure that WP-SpamFree doesn't interfere with the functionality of other plugins. In fact, when other plugin authors have contacted me to let me know of a conflict, I listened, and released fixes within a day. I think other plugin authors need to do that as well.
If you do end up having a problem with WP-SpamFree, please don't automatically assume the plugin is broken. I've been troubleshooting this for a while now and most of the time, it's due to improper installation or a conflict with another plugin that isn't coded well. The first thing to do is go through the Troubleshooting Guide and follow the steps listed there. 99% of the time, it will help you figure out the problem.
Then, if you still can't get it working, contact me through the Support Form, and I'll work with you to figure out the problem.
The reason I ask everyone to contact me through the support form is so that I can dialog with you to figure out what is causing the problem. I will need to get info about your WP Version, Plugins installed, server setup (including PHP version), etc. Some would prefer not to share this publicly (for security reasons, etc.) so, by contacting me through the proper channel, we can discuss this in private and figure things out quickly - to your benefit.