This is on Windows 8.1.1 x64 Pro (latest MS hotfixes), DisplayFusion V7.0.0.B12. Three monitors 3-1-2 with 1 being the main monitor and is Dell P2714T touch screen.

1. Monitor 1 has vertical taskbar, right side, auto hide disabled.
2. Monitor 2 has vertical taskbar, left side, auto hide enabled.
3. Monitor 3 has vertical taskbar, left side, auto hide enabled.

On system startup, the shortcut area of the main monitor's taskbar is blanked out and solid white until monitor 2's hidden taskbar is displayed via mouse rollover. This happens on every startup (reboot or cold start) and thus far I only experience it on system startup. It does not happen if auto hide is disabled on monitor 2.

Pics and system info attached.

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(I had left my original post up as a data point in case it might prove useful in the event an error which was somehow related were to crop up, but I doubt it'll be useful any longer.)
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Quick answer: You are correct; it was a separate issue, as you suspected. (My 'Metro' apps are working again.) Thank you for your response.

Longer answer: Exiting DisplayFusion did not change the unwanted behavior, but I'm not sure DF was fully disabled because the DF taskbar remained active on monitor 2, which indicates that a service (i.e. "c:\Program Files (x86)\DisplayFusionService.exe") might have remained active after the DF UI (and its taskbar icon) had been removed from RAM.

Final answer: Either way, I believe it resulted from a registry/permissions corruption and had nothing to do with DisplayFusion. Whew!