Yeah I have a similar problem, but it occurs even when Appodeal's third-party plugin is not included when building with PhoneGap.
The screen is rescaled and there is a blue bar on the bottom, idk what it may be... I have used banners before, but now I don't...
Interesting, never tried it without plugin... so maybe the fix for that must be searched on Construct's side of the plugin.
Hopefully ill find a solution with appodeal actions, simmilar to smart banners in admob's plugin.