What do you mean by "Eventually the map fills in properly."? That it reverts to being fully explored after some time, or that you need to re-explore the same area a certain number of times before it stays permanently explored?
I don't know, I just know later on when I looked at the map, when I had been there before, I was not seeing the black squares prob.
No, the game is still playable of course, but it basically renders the local map more or less useless, at least for me.
The map is more useful when in dungeons, for determining the passages you need to take to get to a desired location/direction. Esp when the area is not so linear, and has multiple paths to take; or when the passage seems hidden to you, you may not be able to make out the entrance except when you look at the map. I have found places this way that I missed the 1st time through. This is more like what you should use the map for.
One place this is particularly true is Tolvald's cave. You should get nearly 282 Glowing Mushrooms (ref: UESPWiki) from this dangerous Falmer-filled labyrinth. If you have <200 you have not been in all of it yet. It is 3 cells ("Zones") deep, if you only seen two of them you missed the nearly hidden entrance to the passage to "Tolvald's crossing." Look on the map in Tolvald's gap for it.
I was also successful at using the map to make sure I found all the areas within Blackreach. Don't google this area, nor look it up on the UESPWiki, it would be too much of a spoiler for anybody. You will enjoy it proper only if you are surprised by it.
BTW, bring a pick axe when you enter Mzinchaleft.
Also, the map is for finding specific house doors in towns.
Skyrim is the best single-player game ever crafted for home computers. Don't let a few minor shortcomings ruin the experience for you.