In case this may help. If I run one script with the default definition of 
"base compile dir", the script works just fine.

In addtion to Theano 0.9.0, I also have these packages:

pygpu                     0.6.9                    py36_0

mingw                     4.7                           1

libgpuarray               0.6.9                    vc14_0  [vc14]

m2w64-binutils            2.25.1                        5
m2w64-bzip2               1.0.6                         6
m2w64-crt-git             5.0.0.4636.2595836               2
m2w64-gcc                 5.3.0                         6
m2w64-gcc-ada             5.3.0                         6
m2w64-gcc-fortran         5.3.0                         6
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gcc-objc            5.3.0                         6
m2w64-gmp                 6.1.0                         2
m2w64-headers-git         5.0.0.4636.c0ad18a               2
m2w64-isl                 0.16.1                        2
m2w64-libiconv            1.14                          6
m2w64-libmangle-git       5.0.0.4509.2e5a9a2               2
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
m2w64-make                4.1.2351.a80a8b8               2
m2w64-mpc                 1.0.3                         3
m2w64-mpfr                3.1.4                         4
m2w64-pkg-config          0.29.1                        2
m2w64-toolchain           5.3.0                         7
m2w64-tools-git           5.0.0.4592.90b8472               2
m2w64-windows-default-manifest 6.4                           3
m2w64-winpthreads-git     5.0.0.4634.697f757               2


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