Are they Images or Graphics? The difference is important.

Here's a simple example of your problem with a 100 by 100 image and a 200 by 200 image:

Export["test1.html", Grid[{{RandomImage[1, {100, 100}]}}], "HTML"]

Export["test2.html", Grid[{{RandomImage[1, {200, 200}]}}], "HTML"]

When I export these and import them again, I get back Images of the correct size.

You are probably using Graphics instead of Images. Most plotting functions produce Graphics. You can turn Graphics into Images using Rasterize:

Image@Rasterize[myGraphics, RasterSize -> {100, 100}]

I would try using this on my plotting functions.