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.
What you were doing when the issue happened Typing in the RStudio for OS X script editor panel Select text Press COMMAND-C to copy or COMMAND-X to cut 2-3 out of 4 times the selected text APPENDS to the clipboard rather than replacing it, as if one had used Alfred's COMMAND-C COMMAND-C double tap. Whether you were able to replicate it a second time by performing the same action Happens 100% of the time. Have had to add RStudio to the ignore apps list for the clipboard feature to be able to use Rstudio reliably --- but that means I can't use my favorite utility with my most freq