I assume that you've been creating your documents with "Primary Text Frame" in your New Document dialog. This puts a text frame on your default Master page that is set for Smart Text Reflow. It can be identified by the icon that appears when it is selected on the Master page as shown in the screen shot below: Any other text frame set up on the Master will have an icon like the screen shot below and will not be automatically set for Smart Text Reflow: When you try to autoflow text in your document pages as you describe then the default Primary Text Frames would prevail. You can, however, make your text frames that are part of your layout into the Primary Text Frames by clicking on the icon shown in the second screen shot with the regular selection tool on the first of your custom text frames. It will then become primary and can be linked to other custom text frames on your master. Delete the original default Primary Text Frame and you should be ok.
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