OS X equivalents for Ubuntu’s genisoimage and qemu-img

I'm not an expert in this area but it seems to me your test is incomplete: Until you've used your ISO image, you don't yet really know if it's missing those 127K. Even on CD (and DVD) devices, there is overhead. Your ISO images represents a LOGICAL representation, not a physical one, and until proven accurate, I would not trust that the various disk reporting tools are giving you just the actual data byte information - the logical; seldom is care given to reporting just the one or the other.

If you made the disk in question from an ISO and you are comparing ISO to ISO, that's one thing, but so far you haven't actually used your ISO so... you've got some more testing to do. Make a disk from the resulting ISO and then make comparisons...

RT

UPDATE: Oops! Silly me: Investigate your error first! What about the messages log? RT

UPDATE 2: Your update talks about the hardware but you never answered the question: What are the error messages trying to tell you? CDs are not nearly as error-free as magnetic disks...

Assuming they're formatted with a filesystem your kernel supports you can mount them by using a loopback mount. A loopback mount allows you to mount a file as though it's a block device.

If you've partitioned the virtual "disks" that the image files represent you'll have to do some hackery with the mount command to loopback mount the filesystems in the partitions. You can see what I'm talking about in this article. Basically, you're telling the mount command to seek a specified offset into the file. That offset corresponds to the starting location of the partition inside the file.