"Gparted" is a very good tool for partitioning USB-Sticks ... if they are recognized as harddisks !. "Shipped" by the manufacturer they may be formatted either as "superfloppy" (no MBR) or "ZIP-drive" (less than 63 blocks between existing MBR and PBR (from some few up to 32 blocks), formatted in FAT16 or FAT32 filesystem ... or as removable harddisks (MBR, first and single Partition Boot Record =PBR at block 63 (0x3F), normally NOT with active bootflag). Note, that NTFS with its "journalling" filesystem (continous read-write processes, even if nothing gets stored) "wears" out memory cells on the stick chips much faster than the above mentioned preferred filesystems. And a second advice in that context is not to do any "defragmentation" on USB-Sticks, because the stick software "fragments" every file to avoid wearing out memory cells too soon, it's the wanted normal state.
You can download a little Win tool by HP (hp usb disk storage format utility), which "converts" every stick to the harddisk format. If you do it under Win XP and do NOT choose the boot option (only Win 98 boot possible), setting the bootflag with "Gparted" will do the same job. Its even the fastest way to get a Linux bootable stick. Just copy the files "GRLDR" and "menu.lst" from "GRUB4DOS" to the root folder of the stick and rename "GRLDR" to "NTLDR". Now the Win XP boot records initialize at boot a Linux boot manager, which is able to start Win (98, 2k, XP / the "original" NTLDR renamed to XPLDR or so, if also necessary on the stick; Vista boots with some specialties) or Linux at your choice ...the easieast way to have an emergency start medium for your machine(s)! Of course, you have to edit and adapt "menu.lst", which is a text file (there is a very good pdf documentation for "GRUB", but not included in "GRUB4DOS" distribution with its few examples!). This is my way of having several versions of "GParted", "PartedMagic" and "Puppy Linux" available on one stick, its my "Swiss pocket knife" or "Leatherman" for partitioning !
I do not know, if it works generally, but I had one USB Stick converted to the harddisk format just by copying the MBR of my harddisk to the sticks first block, deleting all partition table entries but the first (bootable). "GParted" noticed a faulty state and corrected it. It could then be partitioned and formatted. Note, that PBRs for Win filesystems from "GParted" are NEVER bootable and can NOT be set "bootable". You have to reformat the partition under Win and set the PBR bootflag manually (for FAT 32, label MSDOS5.0 or 5.1 : byte 0x...40 from 0x00 to 0x80)
As you might already know, Win 2k and XP do not support partitioned USB-Sticks, whereas Win 98 and ME have no problems at all. But there is a very small driver from Hitachi (hitachi microdrive filter driver), which solves the problem by simulating non-removable harddisks. The only difficulty is to adapt the INF-File, because you have to fill in the individual HardwareID (e.g. USB\VID_xxxx&PID_yyyy) of your stick. If your stick is plugged to your machine, you find it in device manager properties of the stick (details). If the INF-File of the driver is prepared, choose "update driver" in device manager and the location, where both driver and INF-File are stored, then select "Hitachi Microdrive" and discard the usual warnings. That's all. You can even install a complete, working Win XP on such a prepared stick (copy the content of the CD to the first, bootable partition, install it on the second partition, the fastest way. Note: Mark your HDD temporarily as Linux filesystem / ID 0x83, that it gets not involved; disabling it by the BIOS is NOT sufficient.)!