Something doesn't sound right with what UA has said. I just pulled the Gov't fares on this routing and only 5 fares exist (two of which are military only BMZ and YMZ). In this list, only fares 1, 2, and 5 are valid for non-military Government employees:

BKKWAS-UA 9JUN08 $$ AA AC AF AI AY AZ BA BG BR CI CO CX DL EK
ET EY JL JO KE KL KU LH LX LY MH MS NH NW OS
OZ PK PR QF QR RJ SK SQ SV TG TK VS YY 9W
ADD TAXES * FED INSP FEES
FOR OTHER APPLIC FARES SEE >4F*-YY*UA(
SEG/PFC CHARGES MAY APPLY
LINE FARE RT FARE TRAVEL DATES TKT DTE RTG AP MIN/ BKG
NBR CODE OW USD EFF DISC FST/LST NBR DT MAX CDE
1 VCA 600.00 1APR8 1OCT8*L 1OCT 469 - - / - V
2 YCA 698.00 1APR8 1OCT8*L 1OCT 469 - - / - Y
3 BMZ 1185.00 1APR8 - - 850 - - / - B
4 YMZ 1270.00 1APR8 - - 850 - - / - Y
5 DCB 2617.00 1APR8 1OCT8*L 1OCT 469 - - / - D
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V class is available on the flights through NRT, so the V fare should be used. I have double checked inside UA's own system (via WorldSpan DirectConnect to Apollo) and confirmed these fares are the only ones that exist. I am curious to know what fares UA is using to give you this fare difference?