First, change one or two settings at a time. Respring, see if you like it. If you add too many at once, you may not be certain of what is jacking up your layout.
Second, the developer is updating the apps and releasing an update every few days...make sure you look for them. One fixed the row spacing (I had 4 rows of apps and a 5 row layout crunched all four rows into the top half of the screen). I found another bug where changing the badge background/text color makes the number on the first badge the same number on the rest of the badges. Mine is my calendar app (Calengoo), so app updates, YouMail, Mail, anything I get a notification on, all say 30 today. I emailed him, so hopefully he addresses it as he did the layout when I e-mailed him.