What codec did you use in your MOV container when you rendered out of AE?
When you play that MOV back, do you see white frames?
What were your settings in the Adobe Media Encoder when making your H.264?
If you play that file, do you see the white frames?
(If you're putting it into Flash, I'd recommend using the FLV option in AME.)
No, it's not 'white frames' as much as a few frames of 'blank', as if it wasn't there. The 'blank' is not in the Flash timeline, and it's not in the After Effects timeline, nor in the mov.
I used to use the FLV export in After Effects, but it was eliminated (because it's "old" and "buggy") in the CC 2015 update, so the only option left is to export in H.264 / mp4. I don't really care what format it is, just as long as it isn't heavy, and it can be imported into Flash.
I wouldn't use AE to do FLV. You can do it in old versions of Adobe Media Encoder.
If it's not happening in the rendered file, perhaps it's not an After Effects question.
Where are you when you actually see the missing frames?