Unable to align map

I've tried using snap to grid numerous times, but no matter what I do, I get maybe 3 or 4 rows of map aligned but then the rest is misaligned. I've tried resizing map, zooming in to make sure I'm outlining just a 3x3 square,etc. Still won't align whole map. What am I doing wrong?

Can you post a screenshot of the problem you are having?

If you are using a pregrided map that you uploaded, it is more than likely the grids on your map are not truly spaced properly such as you get the top left corner going just right but the bottom right corner is way off and you go back and forth trying to fix it. It is frustrating but there are a few options you can do if this is the case. Turn off the grid and let the players use the grid on the map much like you would on a table itself. Get the map aligned for most of part then resize the roll20 grids to half of what you have them at then change them to the transparency color. This will give you a more finer movement control also. You will have to fiddle with the distance scaling option also (same page menu as changing the grid size) to get your distance close to what you want. Or you can ignore the grid that is on the map. This is all based on the assumption your map is pregrided.

Pat, that is a good description. 1 and 2, are very useful techniques.  I like 2 the best (and have done that many times in my games, it works well or actually it works better).