What's the profile name? I have a PD-iPhone profile, but no Ipone profile.
Edit: ah, I see you do mean PD-iPhone, having edited your original post
I don't know why you're getting better results with Handbrake. You really need to do some further research or get help from someone familiar with Megui & Handbrake, who encodes for such devices. I've never used Handbrake myself, nor baseline with x264.
OTTOMH however, I'd be more inclined to compare x264 command line options first, before looking at any preprocessing the two apps are doing.
I still suggest you post more details when you can though, as I imagine any reader who can help is more likely to, the better you define the problem.
Best of luck.