I'm pretty sure my batch (should) have no problem, seeing that if you just run it normally from explorer all the start commands works, as the target program are all called as relative path.
It's just that when it is called by your parameter it seems to have lost track of its "starting location" or something. I wouldn't think we need to examine the sif file as even not in installation mode I'm unable to get my batch to perform as it should with your command there, so it's doubtful that it's an installation issue.
But here's the two file you requested: I changed the sif to have it run at T-9 instead of GuiRunOnce, but that shouldn't matter since the same problem of my batch not finding directory structure correctly persist. The problem it seems is rather fundamental and I'm not expecting it to change with different timing of the call to the batch.