This happens when using the new settings, like at nz-photo.com:
<horisontalamount type="number" description="Sets the amount of thumbnails horisontally. 0 is auto" range="0,100">5</horisontalamount>
<verticalamount type="number" description="Sets the amount of thumbnails vertically. 0 is auto" range="0,100">5</verticalamount>
<maxamount type="number" description="Sets the maximum amount of thumbnails to display in a single page. 0 is auto" range="0,1000">25</maxamount>
I admit there are some positioning issues I need to look into here. However, I do question why you guys are using these settings? They were originally included so that it was easier to control amount of thumbnails when embedding the gallery into set-size pages, like blogs or other sites. For your galleries, where the width of the stage is variable depending on the users screen, I don't think you should be setting static amounts at all. This means means it will lock to a certain amount of thumbnails which may often be too much on low resolution screens(or even to little on high resolution displays). One of the huge improvements from V1 to V2 is that it controls layout of thumbnails depending on available screen size.
If you want to control it more, then why not use the following settings instead:
<max_width type="number" description="Sets the maximum width for the thumbnails area" range="0,2000">700</max_width>
<max_height type="number" description="Sets the maximum width for the thumbnails area" range="0,2000">600</max_height>
Figure out how much space(700x600 by default) you require to display the amount of thumbnails you want. The benefit of using this method is that it will actually scale down IF the user has a smaller screen. Then it uses the minimum settings:
<min_width type="number" description="Sets the minimum width for the thumbnails area" range="0,2000">200</min_width>
<min_height type="number" description="Sets the minimum height for the thumbnails area" range="0,2000">200</min_height>
You could turn up the minimum values for the width of the thumbnails area, but that would kind of go against the reason of having the setting, which allows the thumbnails area to scale down on lower screen resolutions. If you set the above to 700x600, same as maximum size, then thumbnails will simply not be visible on low screen resolutions.
Keep in mind that the settings above work in cooperation with the thumbnails margin which provides the minimal space around the thumbnails area on any screen resolution:
<margin type="array" description="Sets the margin between the sides of the screen and the thumbnails. TOP,RIGHT,BOTTOM,LEFT">100,100,200,100</margin>
My original viewpoint for thumbnails, is perhaps to aim for a layout which fits snuggly(with enough margin) on 1280x1024. This because most new mainstream lower-end LCD screens have this resolution. However, keeping the thumbnails area dynamic with a lower minimum size, allows users on sizes 1024x768 and 800x600 to view it perfectly also. For users on very high resolutions (>1280x1024), you could increase the maximum size of the thumbnails area, but I think that simply creates too many thumbnails making it uncomfortable.
I can understand the settings and logic around this may be a frustrating. I will of course look into the issue of positioning anyway though.