Those maps weren't normalized properly, is my guess. I didn't normalize most of the maps from the first module. I really should do that. Since I'm short on time these days and converting Tears is my priority at the moment, I'll try to briefly explain the normalization process.
Step 1) Use any software with a ruler to measure an arbitrary number of squares in either direction. The more the better, but they must be full squares. So, for example, measure the exact number of pixels from the bottom of the lowest possible square to the top of the highest possible square. Ignore squares that are cut off. Only count pixels in one dimension, either x or y.
Step 2) Count the number of physical squares that you just measured the length of. At this point, you should have something like this: 943 pixels = 35 squares. This number gives you the current "zoom level" of the map. Divide the number of pixels by the number of squares to give you the zoom level: 943/35 ~= 26.943. The more decimal places you keep, the more accurate the final result is, so don't just round to the nearest integer.
Step 3) Using the same dimension you used for the length count, get the image's TOTAL length in that dimension. In the example above, I measured the y (top-to-bottom) dimension of most of the squares on the map, but I didn't count a few obscured squares at the top because I couldn't tell where one square ended and the next began. The bottom-most square was also not counted because it was cut off. So the height of this image was 1200.
Step 4) Divide the total height by the zoom level you obtained earlier. This gives you the total number of squares the image REALLY has. In my example, I would do: 1200/26.943 = 44.538. My image has 44 and a half real squares.
Step 5) Decide what zoom level you want to normalize the map to. I always use 50px. Multiply the result of Step 4 by this number. So 44.538 x 50 = 2226.9235.
Step 6) Resize the image. Make sure your editor's "Maintain aspect ratio" option is enabled. Change the value of whatever dimension you were using to the result of step 5. I was using y, so I'm changing the height of the image to 2227. This time you have to round to the nearest integer. Hit OK, and the software will resize the image. Every square will be exactly 50px, or close enough that maptools won't be able to tell the difference.