I do not have Rcmdr installed but looking at a YouTube video https://www.youtube.com/watch?v=oAjC_8PLZxI it looks like the basic command is:
Boxplot( v1 ~ v2, data = mydata, id.method = "y")
You might want to try changing the id.method to "n" . Type this into the script window:
Boxplot( v1 ~ v2, data = mydata, id.method = "n")
Alternatively since Boxplot looks like a wrapper for boxplot you might
boxplot( v1 ~ v2, data = mydata
Note *boxplot* not *Boxplot*
Otherwise we need an Rcmdr expert.
Can you copy the code that is output in the script window and post it here?