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prj file and towgs84 parameters

I have two shapefile layers with identical prj file, but when I open
the first one
in QGIS Properties/General I see "EPSG:23031 - ED50 / UTM zone 31N"
defined as
+proj=utm +zone=31 +ellps=intl +towgs84=-87,-98,-121,0,0,0,0 +units=m +no_defs
(which is what I want)
while when I open the second one it indicates
"USER:100012 -  * Generated CRS (+proj=utm +zone=31 +ellps=intl
+units=m +no_defs)"
Where in the shapefile set is this information kept? I thought all CRS info was
included in the prj file.

I make the second layer in R and write it with writeOGR from an Sp Pol
DF which projection is correct (I think):
 > wpflPR201110_700SPDF at proj4string
CRS arguments:
 +proj=utm +zone=31 +ellps=intl +units=m +no_defs +towgs84=-87,-98,-121


Agus