Splitting up point input by day/month

In the future, I need to assimilate aircraft data, which are numerous (AMDAR tracks have 10,000 to 15,000 samples per hour). So we need to split the input and output by day or month. I will try this out with the CO+CO2 tracer combination. Without any split, this is the reference gradient test:

     alpha               J_bg              J_obs              J_tot                DJ1                DJ2         DJ2/DJ1       1-DJ2/DJ1
         0  2.20800000000e+04  2.18215952442e+04  4.39015952442e+04  2.53570056323e+05  0.00000000000e+00               0  1.00000000e+00
       0.1  1.88748350549e+04  3.88561223537e+04  5.77309574085e+04  2.53570056323e+05 -1.38293621644e+05     -0.54538625  1.54538625e+00
      0.01  2.16453769801e+04  2.01123813788e+04  4.17577583589e+04  2.53570056323e+05  2.14383688526e+05      0.84546138  1.54538625e-01
     0.001  2.20353966328e+04  2.16165471919e+04  4.36519438246e+04  2.53570056323e+05  2.49651419543e+05      0.98454614  1.54538625e-02
    0.0001  2.20755282526e+04  2.18007491723e+04  4.38762774249e+04  2.53570056323e+05  2.53178192645e+05      0.99845461  1.54538625e-03
     1e-05  2.20795527112e+04  2.18195072243e+04  4.38990599355e+04  2.53570056323e+05  2.53530869955e+05      0.99984546  1.54538627e-04
     1e-06  2.20799552700e+04  2.18213864081e+04  4.39013416780e+04  2.53570056323e+05  2.53566137668e+05      0.99998455  1.54539346e-05
     1e-07  2.20799955270e+04  2.18215743602e+04  4.39015698872e+04  2.53570056323e+05  2.53569664637e+05      0.99999846  1.54468371e-06
     1e-08  2.20799995527e+04  2.18215931558e+04  4.39015927085e+04  2.53570056323e+05  2.53570024506e+05      0.99999987  1.25474873e-07
     1e-09  2.20799999553e+04  2.18215950353e+04  4.39015949906e+04  2.53570056323e+05  2.53570040513e+05      0.99999994  6.23479134e-08
     1e-10  2.20799999955e+04  2.18215952233e+04  4.39015952188e+04  2.53570056323e+05  2.53568723565e+05      0.99999474  5.25597506e-06

If I now use the new code, but use 'a' as the point split period, i.e., all observations in one file, I get:

     alpha               J_bg              J_obs              J_tot                DJ1                DJ2         DJ2/DJ1       1-DJ2/DJ1
         0  2.20800000000e+04  2.18215952442e+04  4.39015952442e+04  2.53570056323e+05  0.00000000000e+00               0  1.00000000e+00
       0.1  1.88748350549e+04  3.88561223537e+04  5.77309574085e+04  2.53570056323e+05 -1.38293621644e+05     -0.54538625  1.54538625e+00
      0.01  2.16453769801e+04  2.01123813788e+04  4.17577583589e+04  2.53570056323e+05  2.14383688526e+05      0.84546138  1.54538625e-01
     0.001  2.20353966328e+04  2.16165471919e+04  4.36519438246e+04  2.53570056323e+05  2.49651419543e+05      0.98454614  1.54538625e-02
    0.0001  2.20755282526e+04  2.18007491723e+04  4.38762774249e+04  2.53570056323e+05  2.53178192645e+05      0.99845461  1.54538625e-03
     1e-05  2.20795527112e+04  2.18195072243e+04  4.38990599355e+04  2.53570056323e+05  2.53530869955e+05      0.99984546  1.54538627e-04
     1e-06  2.20799552700e+04  2.18213864081e+04  4.39013416780e+04  2.53570056323e+05  2.53566137668e+05      0.99998455  1.54539346e-05
     1e-07  2.20799955270e+04  2.18215743602e+04  4.39015698872e+04  2.53570056323e+05  2.53569664637e+05      0.99999846  1.54468371e-06
     1e-08  2.20799995527e+04  2.18215931558e+04  4.39015927085e+04  2.53570056323e+05  2.53570024506e+05      0.99999987  1.25474873e-07
     1e-09  2.20799999553e+04  2.18215950353e+04  4.39015949906e+04  2.53570056323e+05  2.53570040513e+05      0.99999994  6.23479134e-08
     1e-10  2.20799999955e+04  2.18215952233e+04  4.39015952188e+04  2.53570056323e+05  2.53568723565e+05      0.99999474  5.25597506e-06

So at least those two are the same! If I now split up the input by day:

     alpha               J_bg              J_obs              J_tot                DJ1                DJ2         DJ2/DJ1       1-DJ2/DJ1
         0  2.20800000000e+04  2.18215952442e+04  4.39015952442e+04  2.53570056323e+05  0.00000000000e+00               0  1.00000000e+00
       0.1  1.88748350549e+04  3.88561223537e+04  5.77309574085e+04  2.53570056323e+05 -1.38293621644e+05     -0.54538625  1.54538625e+00
      0.01  2.16453769801e+04  2.01123813788e+04  4.17577583589e+04  2.53570056323e+05  2.14383688526e+05      0.84546138  1.54538625e-01
     0.001  2.20353966328e+04  2.16165471919e+04  4.36519438246e+04  2.53570056323e+05  2.49651419543e+05      0.98454614  1.54538625e-02
    0.0001  2.20755282526e+04  2.18007491723e+04  4.38762774249e+04  2.53570056323e+05  2.53178192645e+05      0.99845461  1.54538625e-03
     1e-05  2.20795527112e+04  2.18195072243e+04  4.38990599355e+04  2.53570056323e+05  2.53530869954e+05      0.99984546  1.54538630e-04
     1e-06  2.20799552700e+04  2.18213864081e+04  4.39013416780e+04  2.53570056323e+05  2.53566137653e+05      0.99998455  1.54539919e-05
     1e-07  2.20799955270e+04  2.18215743602e+04  4.39015698872e+04  2.53570056323e+05  2.53569664565e+05      0.99999846  1.54497065e-06
     1e-08  2.20799995527e+04  2.18215931558e+04  4.39015927085e+04  2.53570056323e+05  2.53570024506e+05      0.99999987  1.25474873e-07
     1e-09  2.20799999553e+04  2.18215950353e+04  4.39015949906e+04  2.53570056323e+05  2.53570025961e+05      0.99999988  1.19736059e-07
     1e-10  2.20799999955e+04  2.18215952233e+04  4.39015952188e+04  2.53570056323e+05  2.53568796325e+05      0.99999503  4.96903433e-06

It's almost the same, but not quite. Why?