To directly address your question, when I had an issue like this it was because I had saved but not applied my settings in squidblock. Also, I found making a whitelist easy and effective for specific URL's that are being blacklisted I don't want blacklisted. Easy instructions located here > http://doc.pfsense.org/index.php/SquidGuard_package bottom of page, "Exclude domain/URL from blacklist" section.
To address your original inquiry, just wanted to put in my 2 cents for anyone who may be going through a similar struggle.
I was experiencing somewhat similar issues. I realized that my ram began running out and was beginning to use swap.
What I've done which worked great was to remove the pfblocker package with all blacklists there. Now I just use pfsense/squid/squidblock (with the blacklist here http://squidguard.mesd.k12.or.us/ i strongly prefer… all others I was able to find unfiltered porn sites with a simple google search -- found them on the first page of results, actually).
The blacklists I use are ads and spyware, this method is far superior to pfblocker for my needs. It not only seems to perform much faster, but it also is extremely useful to give an error message with the included blacklist that's causing the block, rather than just being unable to reach a page completely. I also have found that the blacklist is good enough for my needs to stop using HVAP which has also improved performance.
Just my experience, YMMV. Good luck.