INSERT - Inside Security rescue toolkit

I used cdisk to partition a USB pen drive into two partitions. The first
is a DOS partition and on the second I've tried both W95 and linux. Then I
used the "install-usb..." menu item to install INSERT on to the device. It
booted and worked as expect. However, I then created a file system on the
second partition of the device (I tried both dos and ext2), mounted the
partition, copied files to it, and finally dismounted the second partition.
When I went to reboot, the pen drive would no longer boot. I installed
the pen drive into a linux box and was able to mount both partitions on the
device and everything looked OK. I ran fsck on both partitions and it did
not report any problems. Just for completeness, I used fdisk to check to
make sure the partition table was still valid and that the first partition
was still marked bootable. Everything was as expected. Should the second
partition of the USB device be usable?