I have just been using different methods for creating Live USB namely Unetbootin,Multi System,Universal USB Creator,LiLi, "dd" etc.

I have just come across the concept of "Super Floppy Formatting" (only 1 partition for the entire drive)..I read that for some apps listed above, the USB to be partitoned as a Hard Disk for the ISO to work .It seems windows recognises all flash drives as "Removable", so the idea is to trick Win to believe that it is a HDD.

I think only Lexar partitioning utility takes care of the above..I guess even HP USB formats as a "Super floppy" format

Currently , I use mkdosfs -F32 /dev/sdx for creating a FAT32 partition..Should I once again create a sub partition to format as USB-HDD?

So for example if ur usb is /dev/sdb,you have to create partition table (MBR) ,then
create another F32 partition (gets created as /dev/sdb1
)
Also most of the apps have formatting option ..Would that not take care of the above? I am confused

Has anyone encountered such problems in creating Single/Multi Boot USBs?

If you want to try application that make "supper floppy" (also called chameleon mode) check out linux puppy.

See pendrivelinux.com for ways like grub4dos.

This might be what you are looking for:

If you are having trouble booting on the usb bar, this might be due to your MBR being corrupted. In order to fix it up, you can use lilo (I installed lilo on my box only for thid purpose).
$ lilo -M /dev/sdb
will fix the MBR on device /dev/sdb

From this article

How To