I've had similar issues to this, and yes, it was PeerGuardian that triggered them. I found various browsers - Firefox, Chrome, Safari, Opera - stopped connecting to some sites. The sites were generally 'big' sites - Wikipedia, BBC, Internet Archive, IMDB, Apple, etc, not sites where you'd expect server failure or overload on catastrophic scale, and not all at once!
The problem turned out to be PG. I'm running 1.6b2 (if anyone has a stable, more recent version for Mac, let me know!), and occasionally as PG tracks and records, it goes nuts.
A good pointer that I'm going to have trouble is that when I start PG, it shows no sites in the 'blocked' list in the log.
To start PG I open the Application folder, and click on PG, then 'show package contents', open the Resources folder, and double click each of pploader.app and pplogger.app. I also took those two out of the auto-start list on my account settings. Then I launch PG from the Application folder, and I'm up and running. I only launch once, when I boot the machine, otherwise it runs quietly in the background. I'd also advocate seeking to update the blocklists when you launch the application.
When there is a problem with it not blocking at all, or blocking out the browsers, I shut it all down and uninstall PG - do this with the uninstaller in the download it came in, and be sure you got it all out! Also, go to MacintoshHD>library>LaunchDaemons and remove something with a name like xxx.qnation.PeerGuardian.kextload.plist. NB Sometimes just shutting it all down, removing this, and starting again will fix the problem.
A re-install of PG, and update of the lists - use
http://www.iblocklist.com/ as a good place for up-to-date blocklists and install them as appropriate in PG, and you're ready to go. Some of the lists that come with downloads of PG are out of date and no longer maintained or even available for update, so worth checking around. The whole process usually takes 10-15 mins, and you don't have to 'unblock' one of those undesirables lists.
It
is a bit of faff, but I like to know it's working. As I say, if anyone knows a more recent version of PG for Mac that is stable, let me know! But it's not much to ask for some privacy and security.
JRJ