I put the data from two scans into different variables but they look the same. Why?

The extmats such as RSS$scan.mat use persistent storage, so the following won't do what you expect:

x <- RSS$scan.mat
rss.process.one.scan()
y <- RSS$scan.mat

In fact, x and y refer to the same storage and so have the same data, which you can confirm by doing:

all(x[] == y[])

To get around this, you need to force conversion of the data to a native R matrix by using indexing like this:

x <- RSS$scan.mat[]
rss.process.one.scan ()
y <- RSS$scan.mat[]

The tendency for R to copy objects is one reason radR uses extmats for large matrices.