The file name without the number is the default map. The ones with numbers are the "user" maps. You have to select those numbers on the map window for them to show up. The ones you download from Mapfiend are defaulted to the "1" slot but you can easily change that by changing the file name...I usually make all my maps the default slot. The only exceptions would be if you want new versions of the maps that come with EQ, because if you change those default ones the game will re-download them when the Patcher runs. (I think the Mapfiend forum is where all the instructions are, by the way.) Any zone that you have ever been to will have the 1-2-3 files created the first time you go there, although they will all be empty until you overwrite it yourself. Anyway, like I said, on the map UI window you can select or deselect the main and 1-2-3 maps, so check those out first. It may be defaulted to deselect the user maps.
The only other possibility I can think of is a simple one: are you too far zoomed in? Sometimes the map zoom changes when you zone.
If you get it to work, and think that the color schemes suck on the user-made maps, you can use a program called
Mappie to change all instances of one color line at once. It's pretty cool for some of those maps which were done by someone with a different color map background than the rest of us. (Although I think some of them are light colors intentionally so the map is like an overlay when it is faded.)
Game on,
The Oneiromancer