Do both frames have the same first baseline offset type and amount, and the same vertical justifcation set in the Text frame options?
Is this a legacy file converted to CS6?
Yes they both have vertical justification set to top, paragraph spacing limit set to zero.
Both set to ascent 'minimum 0'
Not a legacy file - a totally new creation.
Can you possibly sahre a sample page as a .indd file? I think we need to see the real thing to get to the bottom of this.
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It looks to me like this has to do with some settings for Japanese text that have found their way in. They appear in the list of overrides to the paragraph style when you hover over it with the cursor in some position, but not others, and they seem to be tied to the Header_W character style in some way that I can't determine. I don't honestly, understand WHY this is affecting the frames differntly, either.
The only thing that seemed to work for me was to put the cursor in one of the left frames where the alignment is correct, remove the overrides by Alt (Opt for you) clicking the paragraph style name, then right-clicking the style name and choosing redefine. You'll need to also remove the overrides from the other paragraphs and you can do this with find/change by leaving the find and change fields blank and going to the find and change format options (the two magnifier glass icons next to the largish boxes at the bottom of the dialog) and choosing the paragraph style from the dropdown, then change all.
This is probbly going to mess up the type a bit -- I think you've added a stroke that disappeared, but it's hard for me to tell becasue I don't have your fonts. If there are things like that which are missing and should be applied to all but special text in these paragraphs, add them to the paragraph style. The character styles seem to be applied haphazardly, with some having overrides to the character style, too, and I can't tell which ones are working for you and which are not without doning a lot more study, which I don't really have time for this morning. The bottom line is that text should be styled with a paragraph style that applies the basic format for the majority of the text in the paragraph without any need to override it in any way, and "special" types of text should have character styles defined that alter the text to change only those things that need changing -- font family but not size, if that's the change, or family and character color, and so forth, and if you need more character styles to accomplish all of the combinations, create them. I'm not seeing patterns here that jump out, so it's likely you'll need to apply the character styles manually to selected text rather than as nested or GREP styles.
When things are properly styled, you should be able to click anywhere in one of these paragraphs without a + sign appearing after a style name, and your spacing should fall into line.
Thank you for having a look at it. I will try the things you have suggested.