OK, I spent hours trying to figure out why I had extra space between my caption and the table. I'll share my findings here for the next guy.
I have 2 tables side by side in a floating table environment. Each table is in a minipage with the captions on top and an hfill between them. Everything is pretty much identicle on each table. I even checked the .lyx file and all the commands are the same, but on 1 of the tables, the caption is much further above the table than the other.
To get the tables side by side, you have to set the width of minipages so that their total is less than 100% of the column width. It won't set this for you. Apparently, if you don't set it, the default is 100%.
If you set the width too small, it prints the tables anyway. You'll never know. I had both set to 45%. The hfill between them kept the spacing nice. However, an extra line is placed between the caption and the table if the table is larger than the minipage and spills out of it. I turned on "Simple Frame" on the minipage/box to see this effect and thats when I realized what was happening. I have no idea why it adds another line, but it does. It ruins the formatting and cost me hours trying to figure out why because it otherwise looked fine and generated no warnings. Expand the minipage, no more problems, looks great.