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Two column pdf isn't supported in Calibre. There is work underway to support it, but no telling when it will be ready.
Pages epub support has already been reported to be pretty buggy, and you may be seeing some effect from that. If you're just going to do it by copy/paste you could try Sigil instead.
I think others have reported that Mobipocket Creator can create mobi files directly from two column pdfs.
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