Okay, my HDL went up a little and my trigs went down a little but oh my good golly gosh look how much my LDL and total went up. And my apoB levels are kinda scaring me too. I eat very strict Paleo but with dairy (full-fat Greek yogurt and grass-fed butter/ghee). I'm not low carb at all.
April, I would recommend talking to someone with more experience in the field, not a bunch of people on the internet. Kurt Harris doesn't give medical advice over the internet, but he may know someone in your area, or make suggestions about how to find someone in your area. Chris Kresser does do consultations. Stephan Guyenet, Chris Masterjohn, Paul Jaminet: I would be much, much more confident about their advice than a random paleohacker.
The only thing I can write is that it appears that some people experience a rise in TC after going Paleo. I personally have experienced a decrease in LDL and a rise in HDL.
As well, I have yet to read a satisfactory explanation as to why this occurs except for the fact that people are different and have different reactions to how they handle specific foods. Maybe you could begin to slowly remove certain foods from your diet and see the practical results in a lipid test.