For anyone that may be having an issue like this check to see if you are using the "Meta Box Columns" plugin. If so, make sure all your columns add up to 12 on each row. If they don't you'll have a bad time.
After reviewing the 40 meta boxes I've created on my site I found that the very last 3 meta boxes were set at 6, 6, and 6. I was able to fix this by changing that last 6 to a 12.