When ever I am doing many updates and installs it runs into these errors in transaction:
Here for example is what happens when I attempt to update gcc

/nTransaction Check Error: file /usr/share/man/man1/fastjar.1.gz from install of libgcj-4.1.1-1.fc5 conflicts with file from package libgcj-4.1.0-3
file /usr/share/man/man1/gcj-dbtool.1.gz from install of libgcj-4.1.1-1.fc5 conflicts with file from package libgcj-4.1.0-3
file /usr/share/man/man1/gij.1.gz from install of libgcj-4.1.1-1.fc5 conflicts with file from package libgcj-4.1.0-3
file /usr/share/man/man1/grepjar.1.gz from install of libgcj-4.1.1-1.fc5 conflicts with file from package libgcj-4.1.0-3
file /usr/share/man/man1/grmic.1.gz from install of libgcj-4.1.1-1.fc5 conflicts with file from package libgcj-4.1.0-3
file /usr/share/man/man1/grmiregistry.1.gz from install of libgcj-4.1.1-1.fc5 conflicts with file from package libgcj-4.1.0-3
file /usr/share/man/man1/jv-convert.1.gz from install of libgcj-4.1.1-1.fc5 conflicts with file from package libgcj-4.1.0-3
(It apears the newer version "Is conflicting with the old version of the file" and yum gets very confused)

As far as I can tell this only takes place on my fedora core 5 64, I have not encountered it on my 32 bit install. I am running this on a new asus a8v, with amd x2. I have reinstalled many times and the problem presists.
Any solutions or similar experiences will be greatly apprectiated.

Yep this is a common problem on a mixed mode system (both x86 and x86_64 rpm packages installed). Some of the conflicts are because of the version of yum being used and/or the repos configured as enabled. The default installation also installs many x86 packages that are not needed (some are but not as many that get installed).

Step one first update yum; yum update yum

Step two update a bit smarter when you run into one these confilcts try and see if yum can handle this for you with a little assistance from you, for example;

yum update gcc libgcj-4.1.1-1.fc5 libgcj-4.1.1-1.fc5.i386

Take the time and remove many of the x86 application you know you do not need and/or use. Take your time and do this by first testing if the package(s) are needed by something you want/use first, for example;

rpm -e libgcj-4.1.1-1.fc5.i386 --test

A general good rule of thumb: if unsure or you don not know then leave it installed.