So, long story short, I copied Eagle's standard RCL library to prune it down to the SMD essentials and to verify the packages. I removed the old library entirely, so it's not even loaded anymore, and loaded mine and replaced all relevant components in my schematic with a new version from my library.
Now, when I updated the schematic and told it to do a library update, it updates my board. That's fine. However, when I run a ratsnest, it unties the ground pads from the ground plane. What used to be 3 "prongs" from the pad tied to ground from the ground plane is now a single "prong that isn't even fully attached. Also, the ground plane will no longer run between the pads like it would before on the top side... and it puts a hole in the ground plane on the other side of the board.
I'm completely baffled on what would cause this. It's happening consistently with the packages I've modified. The only things I've changed are: updated pad sizes, moved the outline of the actual part to the Dimension layer, and added a courtyard in both tKeepout and in tPlace. I tried removing the courtyard lines from tPlace/tKeepout to no avail.
Here's a picture of what Eagle is doing:
Please help. I'm so friggin' baffled. :(