You can set Samba's filename case sensitivity in /etc/samba/smb.conf. From man 5 smb.conf,

The options are:

mangle case = yes/no
        controls if names that have characters that aren't of the
        "default" case are mangled. For example, if this is yes
        then a name like "Mail" would be mangled. Default no.

case sensitive = yes/no
        controls whether filenames are case sensitive. If they
        aren't then Samba must do a filename search and match on
        passed names. Default no.

default case = upper/lower
        controls what the default case is for new filenames.
        Default lower.

preserve case = yes/no
        controls if new files are created with the case that the
        client passes, or if they are forced to be the "default"
        case. Default yes.

short preserve case = yes/no
        controls if new files which conform to 8.3 syntax, that is
        all in upper case and of suitable length, are created upper
        case, or if they are forced to be the "default" case. This
        option can be use with "preserve case = yes" to permit long
        filenames to retain their case, while short names are low
­         ercased. Default yes.

Those can be set globally or per-share.

Nothing much to be done about the win32 box not caring when it looks up files, though.