Last night after trying again to fix this, I recreated the map on a blank page and uploaded it to the server, and it worked fine.
I then applied my DW template to the page, and uploaded it, and once again I had the problem in IE of the map only half displaying, or having the wrong zoom (zoomed way out).
After trying one thing after another, I discovered that when I had the map div inside a table cell that is behaved strangely. I removed the table, and used floated divs and the problem went away.
I don't know if this is the same issue that you are experiencing, but it worked for me.