Hello there, stbuckler.
We haven't received similar issues with KY UI-3 filing in QuickBooks Online (QBO).
Since Community is a public space, I want to ensure your account information remains secure. I recommend getting in touch with our QuickBooks Payroll Support Team so they can check your account and investigate why the amount changes when submitting to KY UI-3.
You can reach them through this link: https://payroll.intuit.com/support/contact/?infosrc=qs&service=64
Please stay in touch if there's anything else I can help you with. I'll be around to help you in any way I can.