I tried installing a "pen drive" version of Ubuntu from PenDriveLinux.com, but since it was a modified version of Live Ubuntu (i.e. that usually runs from a CD), it had some kind of custom "persistence" options that made some parts of the file system readonly. What I am looking to do is boot from my USB and have the distro work exactly like a "regular" distro - i.e. be able to write anywhere I would normally be able to and have it persisted, install packages, etc.
Also I would like to be able to access the filesystem from Windows (i.e. not just mounting the Windows disk while running Linux).
I tried just installing a standard Ubuntu distro to my USB as if it were just a standard drive, but I got what seemed to be some low-level errors (forget what they were). Should this be expected, or should I just try installing some other standard distros.