There are a couple of things you can do, if you go into your Pages section and right click you can enable and disable "All document pages to shuffle", and "Allow selected spread to shuffle".
Also, for your master page, do you have a master page for a left side and a right side? You can click and drag the master page icon from within the Pages window and drop it onto any of your pages and it will assign that master page layout to that page. So essentially you could create new master pages for your layouts and individually assign them that way as well.
Not sure if that helps you or not. I usually don't place text boxes in my master pages, I just have it preset with margins/columns and guides and then I lay down the content as I go along. I usually only use master pages for top, bottom, side, and other consistencies throughout the document. Maybe I'm backwards but I like the flexibility.
Are the text frames snapped to the margin guides? If not, change the guides on the master page so they are, then enable layout adjustment before adding additional pages and you should be OK.
I agree with Peter Spier. When text frames snap to margin or column guides, their position will shift when layout adjustment is enabled (Layout > Margins and Columns). I also agree with whitworth916, who suggested not placing text frames on master pages, as doing so tends to create more problems when changes need to be made.