No; no other keyboard-related apps.
Note that this issue only occurs (for me) with RStudio -- Alfred's clipboard features have and continue to work as expected with all other apps I use.
Also, the problem only occurs when using the COMMAND-C keyboard shortcut; the Edit > Copy menu item works as expected.
I suspect it may have something to do with RStudio's use of QT to provide the text editor; perhaps they're capturing the keypress, then generating a second keypress event to pass through to their UI.