You've got me. I went the Zweigart site and they don't have this linen listed at all, although I see it offered through other online needlework shops. However. Things I've found with linen in the past make me think that your problem is probably just the nature of the beast.
Linen threads are never completely smooth. This means that parts of them are always going to be thicker than others. If you absolutely HAVE to have completely square crosses in every case, 100% linen isn't the fiber you want for your fabric. Usually the variations work out over the course of a project: stitching over multiple threads evens out the stitches and everything comes out smooth, more or less. Sometimes you get a piece of fabric that's more slubby than usual, and you can end up with the issue you seem to be having. When you get into higher counts, sometimes the warp thread will stretch when it's woven, since it's under very high pressure. This can stretch out the count in that direction.
So if you're looking for perfectly square stitches, you want something other than linen. That said, I've never seen evenweave fabrics in threads other than linen that come with a higher count than about 32. This doesn't mean they don't exist: only that I haven't' found them. I've been known to stitch on plain dressmaker's fabric when I need a higher count.
My suggestion for you on this design is to play around a little. Since you seem to have a definite skew in one direction, try stitching over 3 threads warp wise and 4 threads weft-wise, which may square your stitches.
Hope this ramble helped a little!