Erratic Trouble rsyncing between windows share and linux

[Walls Rob W Contr 75 CS/SCBS]

I am trying to rsync between two linux boxes, but one of the linux boxes is
using samba to map a share from a windows SAN onto it's file system. Rsync
quit working properly when I changed the source directory from a local ext3
filesystem to the windows share mapped onto the filesystem. This setup may
be kind of odd, but I need to keep user's data on the SAN and I also need
the linux box to generate dynamic content which is all then mirrored using
rsync to a remote web server. I can't run rsync or ftp directly on the SAN
machine or have any control of the SAN other than file permissions, so I
thought rsync would work just as well as it always has. Well, now old files
are seemingly arbitrarily picked up as needing synchronizing when they don't
and a different set of (also a random set of old files) are picked every run
of rsync. Weird. New files ARE accurately found and synchronized, however.
But, worst of all, seemingly random files are deleted from the remote box,
since I am using the delete option. 
I've heard there is a file mod time resolution difference between linux and
windows, but it seems that would produce more consistent symptoms. 
The only difference between the previous working and current non-working
rsync setups is that now one of the source directories is mapped from a
windows machine (I used mount -t smbfs, because smbmount didn't seem to want
to work either, sheesh). All rsync versions, exclude file contents and
calling syntax is the same. The source directory I'm having problems with
has 100,000+ files and is about 4.5Gb total size.
Does anyone have any ideas as to why this is not working using a samba
share?

Rob Walls