What do you mean it doesn't see them?
When you position the loaded text icon over a text frame, parentheses enclose the icon . Mine still looks like this: . Trying to click where the master text frame is simply creates a new frame on the page.
Likewise, holding shift should cause the cursor have an autoflow arrow within parentheses, but mine just looks like this: . Shift-clicking creates a whole bunch of new frames in the two columns, never recognizing the presence of master text frames.
This behavior contradicts what Adobe says should happen.
Don't know if this is the problem, but if you hold the loaded cursor on a guide of any sort the existing frame will be ignored (as far as I know this is not documented anywhere), so have you tried moving the cursor out into the open middle area of the frame someplace?