The reason why 300 is a better choice is that it's more likely to already be generated, because 300 is the default size of thumbnails. Thus, the probability that requesting a 300 thumbnail for the first time is faster than requesting a 290 (non-standard size) thumbnail is much higher. Which is why requesting a 300 thumbnail is faster on average.
However, not all files have been used as thumbnails of the default size yet, which means that when a person is the first to view a hovercard for a file like that, the 300 thumbnail is generated on the fly.
1. Some images are taking too long to load [3]
There's a small chance that the 300 thumbnail for a given image hasn't been generated yet. In which case the image will take on average (based on our Media Viewer performance measurements) 1 extra second to load. Once one person has seen that hovercard, though, that extra second won't happen again for anyone. If you're seeing a hovercard where a specific image is always slow, this is unlikely to be the source of the issue.
I went to the Monet page and tried that specific hovercard and I couldn't get the image to show up at all. But, looking at Firebug I clearly saw that the image loaded correctly. Therefore, I think the issue appearing on that specific hovercard is something to do with Popups' code, not the thumbnail infrastructure. The image is being loaded, but it's not being displayed on the hovercard.
I would imagine the answer is in PageImages, which I'm unfamiliar with. Have you tried contacting Max, who wrote it, about this issue?