Not sure if this is the ideal solution, but the only way we found around this issue was to change it to force m4v format with PresetPassthrough set. I.e:
exportSession = [[AVAssetExportSession alloc] initWithAsset:[AVAsset assetWithURL:assetUrl] presetName:AVAssetExportPresetPassthrough];
exportSession.shouldOptimizeForNetworkUse = YES;
exportSession.outputFileType = AVFileTypeAppleM4V;
filePath = [title stringByAppendingString:@".m4v"];
Audio and video seems to work fine for videos imported locally this way, after making that change.