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This doesn't surprise me.
However, I am curious if https has a negative effect on SEO. If possible, would it be better to only have the checkout process be under https?
*I didn't see a search, so I apologize if this topic has been discussed 1000 times before. I'm a newb here.
https: also takes longer to load. So, unless you're a bank, where users might want to see the padlock during their entire session, using https: only for checkout is a good idea. Just make sure that once you do this there's no way to leave the checkout area to another portion of your site under https.
This usually happens when your standard navigation doesn't specify a protocol. Therefore the links on the checkout pages use https, while those on normal pages use http. By specifying http:// in your navigation, you eliminate the problem. You might also consider disallowing robot access to your checkout pages in robots.txt.