When you set hotkeys in Tinn-R, it apparently sets some kind of global watch that "eats" that key combination even when Tinn-R does not have focus. This causes problems when using other programs that also use those hotkeys.
For instance, if I set F5 as the Tinn-R hotkey for "Send line", then I can no longer user F5 as a hotkey in ANY other program as long as Tinn-R is running. Tinn-R will intercept that keystroke and send the current line to its R console.
This should be changed so that Tinn-R only interprets its hotkeys when its window has focus (and possibly also when its associated R session has focus).