I haven't done it for a while so had to refer to my notes! Also had to install the software on a machine that I haven't used before. Now.. I used the 2.07 beta version of pony prog and it seemed to work just fine.
I have a screenshot of my settings here and have an idea why it didn't work for you...
After programming, it should then try to read it all back. I think mine stopped at 28% too (but it's a bit fast to see), and then it reads back to verify. My guess is that the hex file only uses 28% of the memory (and hence stops writing here) and that your problem is in the verifying not the programming.
I think, what you may not have done is to set the interface to AVR I/O. Please check my screenshot and compare with your own settings, and let me know what happens.
I see I need to improve this section of the manual as well