It would appear that you have something wrong with the contents of your user configuration directory since it works if we force a new configuration (what the geany -v -i -c .... does, it stores a new default configuration in the /tmp/... directory).

It may be something left over from the old version of Geany.

It looks like you will have to remove the configuration file .config/geany/geany.conf in your home directory with *no* copies of Geany running. After you have deleted it, start a copy of geany normally (do not open a file just start geany), change the Shell: preference to /usr/bin/R, stop geany, start geany and then see if the R prompt is displayed in the terminal.

Cheers

Lex