Which SEEN.TXT are you using?
Are you running in with Japanese codepage set for non-Unicode?

I have posted a stop gap solution, grab a new version of rlBabel from here http://code.assembla.com/clannad/subversion/nodes/current/rlBabel.dll#
Instead of crashing it will report the string is missing or mistranslated.

The actually problem will be fixed later (translate the line), so the ticket remains open.

The untranslated lines are located in the .ke file for both FV and regular. They should moved to a resource file and translated. I'll take of it later if no one else does.

#res<0246>
pause
intF[1101] = 0
intF[1102] = 0
intF[1103] = 0
strS[1001] = 'CGRY11E'
intF[1104] = 0
strS[1002] = 'NONE'
intF[1105] = 0
strS[1003] = 'NONE'
intF[1106] = 0
intF[1113] = intF[1112]
farcall (9050, 0)
intF[1107] = 0
op<1:Sys:00211, 0>
op<1:Sys:00216, 0>
farcall_with (9600, 0, 342902360, 6)
intF[1126] = 1
strS[1017] = 'Ryou'
strS[1020] = 'I... this one, I wonder?'
{「私は…これかな…」}
{I disagree with Kinny Riddle but I'm not a TL...}
intF[1127] = 1
strS[1018] = 'Kyou'
strS[1021] = 'This one, right?'
{「あたしはこれね」}
{I disagree with Kinny Riddle but I'm not a TL...}
intF[1128] = 0
strS[1019] = ''
strS[1022] = ''
farcall (9075, 0)