Comments are back on, but only because post pages are off (Settings > Archiving > Enable Post Pages? = No).
I couldn't find a way to get rid of Blogger comments on individual post pages and use HaloScan instead, but hopefully it's just a temporary glitch. HaloScan will have a solution in a few days.
If you're having similar problems, these two links might help:
Getting Haloscan to work in Beta Blogger (from Logical Philosopher)
I used Steps 1, 2 and 3 to get HaloScan onto the main page here, but Update 2 wasn't any use.
Getting Haloscan to work in Blogger Beta (from Potentate Matthew I)
Recommended by HaloScan.