Sounds to me like you have 'stroke' on some of the text boxes. Even though this can easily be seen in the tools palet it can be overlooked.
If VIEW/SHOW FRAME EDGES is active and a fine stroke is in use the frame edge will hide the stroke.
I'm experiencing the same in the script i'm working on now. It is strange, haven't had time to look into it.
For now i explicitly set the the stroke to zero. That helps.
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