I have experienced the same problem with video files having large key-frames, but not such long lag times.

Unfortunately the only way I can check the key-frame, is to load the video into AVC Video Remaker, and check clippings, where it always is done between key-frames, and have seen large key-frames in some DIVX videos.

I have 2 ways, to get around this.
1: Remaking the video to a h264 file, which is default to Studio.
2: Increase the Optimization Threshold to 90 or higher.

PS: I am running the 32-bit version of Studio instead of the 64-bit, as I found it more tolerant to various codecs.