What platform(s) and device(s) have you tried this on? Include OS version as well. Video might be useful, as well as your config.xml (minus secret/identifying info).
Sorry, I didn't provide much info, did I?! This is an issue affecting Android builds which I have observed on a OnePlus 3 and a Nexus 5, with the same result that the APK from Phonegap Build displays a title bar prior to display of the splash screen, rather than a plain grey background. See the linked videos for a demo. I've also created a bare-bones Cordova/Phonegap app to demo the problem if you want to try for yourself.
OS: Windows 10 64bit
Cordova v6.5.0, Android platform v6.1.2
Tested on Android 7.0 and 6.0.1
Do you have Hydration enabled?
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Yes unfortunately Phonegap Build uses a different template for its AndroidManifest.xml, amongst a few other possible differences. In your specific case, I believe the difference in launch appearance is that by default your local manifest has the NoActionBar theme, while PGB doesn't. Try adding this to your Phonegap Build config.xml:
<config-file platform="android" parent="/manifest/application" mode="merge">
<activity android:theme="@android:style/Theme.DeviceDefault.NoActionBar" />
You can use apktool to unpack your compiled apk files and compare the AndroidManifest.xml files for a few other differences. You can use the config-file element to tweak the AndroidManifest.xml on Phonegap Build. Having the local and remote builds line up a a little better is something we hope for in the not too distant future.
Thanks Ryan, that has solved my immediate issue, and the apktool tip is super-useful too