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I have worked on some continental scale raster and vector datasets and all rasters are saved as Netcdf´s.

This was done by converting rasters with different timestamps and variables to a Netcdf file.

When working on Ubuntu (QGIS 2.14) all vectors and rasters are in the right place but when loading the same data in windows (QGIS 2.16) the rasters get flipped and move out of place.

I have been using EPSG:4326. Below follows and example of the metadata for a file with one raster layer (Which also displays wrongly).

Driver
GDAL provider
HDF5Image
HDF5 Dataset
Dataset Description
HDF5:"G:/Aquaspace/Final/Raster/BATH/BATH3.nc"://BATH
Conventions=CF-1.5
GDAL=GDAL 1.11.3, released 2015/09/16
GDAL_AREA_OR_POINT=Area
history=Fri Aug 26 17:48:12 2016: ncatted -O -a long_name,BATH,o,c,bathymetry BATH.nc Fri Aug 26 17:47:44 2016: ncrename -v Band1,BATH BATH.nc Fri Aug 26 17:46:35 2016: GDAL CreateCopy( BATH.nc, ... )
Band 1
BATH_grid_mapping=crs
BATH_long_name=bathymetry
BATH__FillValue=-32767 
STATISTICS_MAXIMUM=3800
STATISTICS_MEAN=-28506.247088649
STATISTICS_MINIMUM=-32767
STATISTICS_STDDEV=10787.572663429
Dimensions
X: 21601 Y: 10801 Bands: 1
No Data Value
*NoDataValue not set* 
Data Type
Float32 - Thirty two bit floating point 
Pyramid overviews
Layer Spatial Reference System
+proj=longlat +datum=WGS84 +no_defs
Layer Extent (layer original source projection)
0.0000000000000000,-10801.0000000000000000 : 21601.0000000000000000,0.0000000000000000
Band
Band 1
Band No
1
No Stats
No stats collected yet 

Does anyone know what could cause this problem?

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