If you're inserting as MP4, Captivate shouldn't be doing anything to the video itself on publish (as opposed to if you inserted a non-MP4, then Captivate would launch AME to change that video to MP4).
So if that's correct, then there wouldn't seem a reason the video should change at all in the output.
How about this: find the MP4 in your published folder. If you have only one video, it should be the only .mp4 in the published subfolders, but will likely be renamed. Play any MP4 videos you find in the published folder til you find the correct one.
Copy the name of that MP4.
Delete it.
Copy over your original MP4.
Change its name to the name you copied.
So now you know for certain that the video the published CP piece plays is exactly the same as your original (because you just copied it there).
If playback is still dark/different, then it may be something with the browser (?).
If you drag the video on top of a browser window and drop, does the video play? Does it play at the quality you expect?