this seems to get even more worse if you do not modify the fpga image, meaning you leave the image as it is created by quartus before 9.1 and only want to update the epcs images due to application software update.
normaly this is just a batch job that stores the application
after the fpga image in epcs device. even this does not work with quartus 9.1
all epcs files produced by quartus 9.1 here are completly useless
so we keep at least one quartus 9.0 installation to generate the epcs files for jtag or in application programming.
hopefully Altera will release a fix very soon.