Illustrator - Pattern Swatch / Clipping mask issue

I'm currently working in Illustrator CS6. I'm creating pattern swatches and have successfully created 20 - but 4 are giving me the following issue.
When I drag the perfect swatch tile into swatches it appears as so instead of the perfect tile:
"New pattern swatch 3" has a white space on the right. Which sometimes when I create the swatch takes up half of the 'swatch.'
When I go to create a shape and apply the pattern, I am left with an empty box.
When I double click to adjust the pattern I get this dialog box:
When I go to adjust the bounding box, to see where my pattern is - this crazy mess happens:
Further investigation and deleting items to see whats happening:
Bits of my pattern appear, but not sure why the other bars are there.
I'm having this issue with four very different patterns. But I have also succesfully created more complicated ones. Not sure why this is happening.
Any help is greatly appreciated!

Hey everyone,
I am in the same version, same file. I have also tried starting from scratch in another file just to make sure. Same issue.
I have templates of what i want my patterns to be, so I have tried to make the patterns both ways. Starting from my original art - expanding all shapes and making them so they will tile perfectly.
1. with clipping mask. 2. released mask, and expanded shape. 3. perfect tile.
from scratch, made to tile perfectly.
Same issue for both:
To make sure it wasn't only this one I tried a different pattern that was giving me the same error before hand.
I tried with original art which didn't work, so I quickly recreated with squares. Same tile, one time it was empty producing same issue as above. And second time it did this:
1. What tile is supposed to look like       2. Tile applied to shape - but the pattern swatch icon is empty?
Maybe this is a program bug?

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