Concatenating input files changes the Electron Transfer Coupling Energy

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While running Electron transfer calculations on various molecules, I accidently concatenated an input file with itself and got a different value for the Electron Transfer Coupling Energy. I am not sure why this would happen; it should simply rerun the calculation. I reran the calculation multiple times separately, and I get a coupling energy consistent with the single run. I tested this on the benzene dimer:

start test
geometry BENZI units angstroms NOCENTER NOAUTOZ NOAUTOSYM
H 1.21943 -0.16516 2.15996
C 0.68248 -0.09239 1.20875
C -0.70744 -0.03519 1.19732
H -1.26436 -0.06297 2.13935
C -1.38982 0.05722 -0.01143
H -2.48356 0.10214 -0.02044
C -0.68242 0.09248 -1.20876
H -1.21940 0.16520 -2.15990
C 0.70748 0.03523 -1.19730
H 1.26413 0.06285 -2.13946
C 1.38989 -0.05717 0.01143
H 2.48360 -0.10222 0.02049
end
geometry BENZJ units angstroms NOCENTER NOAUTOZ NOAUTOSYM
H 2.47117 -4.36748 -0.36219
C 1.37747 -4.32248 -0.37129
H 1.20697 -4.43048 1.77731
C 0.67007 -4.35768 0.82611
H 1.25167 -4.20248 -2.52219
C 0.69507 -4.23008 -1.57999
C -0.71983 -4.30048 0.81461
C -0.69483 -4.17278 -1.59149
H -1.27683 -4.32828 1.75671
C -1.40223 -4.20808 -0.39409
H -1.23183 -4.10008 -2.54259
H -2.49603 -4.16318 -0.40309
end
geometry BENZIJ units angstroms NOCENTER NOAUTOZ NOAUTOSYM
H 1.21943 -0.16516 2.15996
C 0.68248 -0.09239 1.20875
C -0.70744 -0.03519 1.19732
H -1.26436 -0.06297 2.13935
C -1.38982 0.05722 -0.01143
H -2.48356 0.10214 -0.02044
C -0.68242 0.09248 -1.20876
H -1.21940 0.16520 -2.15990
C 0.70748 0.03523 -1.19730
H 1.26413 0.06285 -2.13946
C 1.38989 -0.05717 0.01143
H 2.48360 -0.10222 0.02049
H 2.47117 -4.36748 -0.36219
C 1.37747 -4.32248 -0.37129
H 1.20697 -4.43048 1.77731
C 0.67007 -4.35768 0.82611
H 1.25167 -4.20248 -2.52219
C 0.69507 -4.23008 -1.57999
C -0.71983 -4.30048 0.81461
C -0.69483 -4.17278 -1.59149
H -1.27683 -4.32828 1.75671
C -1.40223 -4.20808 -0.39409
H -1.23183 -4.10008 -2.54259
H -2.49603 -4.16318 -0.40309
end
BASIS 
* LIBRARY 6-31g
end
SET geometry BENZI
CHARGE 0
SCF
NOPEN 0
UHF
SINGLET
VECTORS INPUT atom OUTPUT BENZI_0.movecs
maxiter 100
end
TASK SCF

SET geometry  BENZI 
CHARGE 1
SCF
NOPEN 1
UHF
DOUBLET
VECTORS INPUT atom OUTPUT BENZI_1.movecs
maxiter 100
end
TASK SCF

SET geometry  BENZJ 
CHARGE 0
SCF
NOPEN 0
UHF
SINGLET
VECTORS INPUT atom OUTPUT BENZJ_0.movecs
maxiter 100
end
TASK SCF

SET geometry  BENZJ 
CHARGE 1
SCF
NOPEN 1
UHF
DOUBLET
VECTORS INPUT atom OUTPUT BENZJ_1.movecs
maxiter 100
end
TASK SCF

SET geometry  BENZIJ 
CHARGE 1
SCF
SYM OFF
ADAPT OFF
NOPEN 1
UHF
VECTORS INPUT FRAGMENT BENZI_0.movecs BENZJ_1.movecs OUTPUT BENZI_0BENZJ_1.movecs
NOSCF
end
TASK SCF

SET geometry  BENZIJ 
CHARGE 1
SCF
SYM OFF
ADAPT OFF
NOPEN 1
UHF
VECTORS INPUT FRAGMENT BENZI_1.movecs BENZJ_0.movecs OUTPUT BENZI_1BENZJ_0.movecs
NOSCF
maxiter 100
end
TASK SCF

SET geometry  BENZIJ 
CHARGE 1
ET
VECTORS REACTANTS BENZI_0BENZJ_1.movecs
VECTORS PRODUCTS BENZI_1BENZJ_0.movecs
end
TASK SCF ET

SET geometry  BENZIJ 
CHARGE 1
ET
VECTORS REACTANTS BENZI_1BENZJ_0.movecs
VECTORS PRODUCTS BENZI_0BENZJ_1.movecs
end
TASK SCF ET


For each case of hole transfer from BENZI-> BENZJ and BENZJ-> BENZI I get:

Electron Transfer Coupling Energy |V(RP)| 0.0026485746

But when I concatenate the above input file with itself and run the calculation I get:

Electron Transfer Coupling Energy |V(RP)| 0.0044280336


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