What kind of theme being utilized should have virtually no effect on any Windows Updates while using UltraUX Theme Patcher. After all, its the service the runs in the background that would have an effect (If any) with the updates.
Are you talking about UXStyle? UltraUXTheme doesn't run a service. If you're running a custom theme after you update the theme binaries (as the IE update does), windows will not start after you reboot (blinking black screen). This has been confirmed by multiple parties and Hoefs himself.