It's difficult to answer without seeing a screen shot but here's what I think is happening. When you change the margins, the page margins change but the text frame that contains the text remains the same size. I'm guessing that if you resize the frame, you'll be back in business. If you were to setup your document using the Primary Text Frame feature, you'd be able to modify the page margins, then adjust the text frame on the master page to contain two columns and then all of your pages would follow suit. I hope this helps.
Here is a screen shot of what is happening.
I have a master page for each of the sections; there are around 9 sections. The only items that I have on the master pages are the headers and the margins are set, but only as one column (See the second screenshot of what the master pages look like). Could the issue be with the margins and not the columns? Not all of the pages have content that is separated into the two columns. Like in the picture below, on some pages, the content spreads across the whole page. When I changed the margins and the columns from 1 to 2, the content shifted. As you can see, the content lines up with the inside margin, but not the outside margin.
You can use Layout Adjustment but:
- All frames MUST align to the border guides.
- All content must be formatted with the use of styles: Paragraph, Character, Object, Table and Cell Styles.
- If you change the number of columns, change it via Object Styles’ frame columns.
You did not align frames to the border guides.
I ended up having to recreate the file and used primary text frames. I should have done my research on it before I added so many pages. Thank you for all of the responses!