Just tested on my system- The only time I have trouble using rect. selection using ctrl-drag is when I ctrl-drag on a function name. Works just like it did in SciTE for me.
I'm running 0.21.0 but with all the commits that depended on GTK>2.10 dropped. Did a log search for "select" between versions 0.20.0 and 0.21.0 and doesn't seem there were any changes mentioning a change in behavior.
-Kevin