sorry this is an old file and I only got the reconstructed psd with hires layer anymore.
BTW: I fixed the problem. As hires easer (or photoshop) seem to have a problem with transparent selection I tried another method.
I made a solid version of the hires layer by adding a simple color under it and merging. And sliced it up.
I used a rename programme to change the last three letters at the end of the filename 'ALL' to 'rgb'
I went back to the original psd. Selected the transparency of my hires layer and filled it with white. Added a black layer under it and merged again, so I got an alpha channel. (A script could probably simply use the alpha channel)
I split it up again to a different folder and again used the rename programm to change the 'ALL' to 'a'
Now I put both sets in one folder and flattend the layers with a batch action (thats because of a plugin limitation)
And voila it worked....
I guess it would be possible to integrate this into hires easer as a special option for transparency issues e.g.
Of course it's not a real fix - just a workaround...
So is this the psd with the transparent tiles or the modified one? I would need the one with the transparent tiles to reproduce the bug. And if you still have the TextureId.txt (or however it was called) mapping file would be great as well.
EDIT: After investigating the script, the bug posted by heroshade might be caused if the tiles that are smaller than the others are located at the end of a row.
As hireseaser uses the dimensions of the first tile to calculate the dimensions of the canvas this might lead to wrong dimensions of the last tiles in a row in this case.
I will apply the corresponding changes hopefully tomorrow. But the reason for your bug seems to be different & is not yet clear to me...
Btw. you did the 100th post in this thread and won a feature at your choise