Here is a screenshot of the problem:

The image is a map of a fantasy nation. The water and land on that map are simple blue and green items with a low opacity. Underneath is a large rectangle that contains the pattern (the object selected to the left is the pattern source.)
I have sort of hotfixed the problem by duplicating the rectangle, giving it the same pattern fill, then flipping it both horizontally and sending it to the back, but I was wondering if there was a better fix.
The pattern is a square but it is not a power of 2 (eg, 64x64 or 128x128.)