ubuntu - Multi-partition USB stick

In my freelance job as "the dude that fixes your computer" I have an extremely handy tool, a bootable USB stick with Ubuntu LiveCD that allows me to recover and investigate in a known, working environment.

Now, I want to reformat this USB stick and reinstall with Casper-RW persistance. I did this a few times before with a FAT-formatted USB stick. It was a horror. The USB drive corrupted constantly, by people accidently removing the USB stick, the computer not properly shutting down, ETC.

Now what I want to create a multi-partition USB stick so I can put Ubuntu on a ext partition, but still be able to store some Windows stuff in it, by having a secondary FAT partition.

However I read somewhere that Windows will only check the first partition on USB sticks, giving a problem with the first bootable linux partition.

Is this possible on some way?

EDIT

Perhaps it wasn't clear what the problem is. The problem is that I read somewhere that Windows will only recognize the first partition on a USB stick. But I want two partitions, a ext partition and a FAT partition. No issues so far, but in order to be bootable the ext partition must be the first one!