So I'm using the following seam fix -

http://mw.modhistory.com/download-90-10353

Pretty popular as we can see, but I'm wondering if there is an updated version because this mod seemed to add more seams in my game. One particular area between Balmora and Caldera is particularly rough -

With fix - http://i.imgur.com/TXvdgkD.png

Vanilla - http://i.imgur.com/ySl3Nmp.png

Another -

With fix - http://i.imgur.com/8707PmW.png

Vanilla - http://i.imgur.com/kzr5DAB.png

Considering the nature of the mod I'm suprised these got through, were they ever fixed in an update?

It's due to the way morrowind landscape modding works. Any time a mod makes a change to a cells landscape it will overwrite the texture fix changes. So unless the mod used texture fix landscapes as its base you will see new seams where the overwritten landscapes border the esm's fixed versions.