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I've been trying to do this for quite a while and I feel like I have exhausted my options on it. I want to make a flash drive partitioned similarly to this:

Number  Start (sector)    End (sector)  Size       Code  Name
   1            2048         2930687   1.4 GiB     0700  Microsoft basic data
   2         2930688        31709183   13.7 GiB    8300  Linux filesystem

First partition is fat32 (readable via windows) and second partition has a native installation of linux (don't care what distro/fs). The kicker is that I'm trying to boot this thumb drive on an HP server which apparently will not boot just any thumb drive. I think it has to be DOS-based. I've tried using grub to boot to the linux partition and it works great on different machines but on the HP machine it complains like this:

Attempting to Boot from USB DriveKey (C:)
GRUB loading.
Welcome to GRUB!

error: out of disk
Entering rescue mode...
grub rescue>

Unfortunately, there are no thumbdrive/harddrive/boot options in the BIOS on this machine. Because it seems that grub is a "no-go" I thought I'd try to use syslinux but syslinux doesn't appear to support booting to different partitions. I have found that using syslinux and memdisk to boot an ISO on the fat32 partition works fine on the HP (like a LIVE iso) BUT I need to be able to customize some things in the linux installation - like mounting the fat32 partition and executing a script on boot-complete.

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