I do remember having the same problem with hotkeys in StrokeIt at some time. But fear not! There are alternatives to hotkeys in the 'Keys - Send Keystrokes' option. Fot example, if you want to use CTRL + V in hotkeys, use [CTRL_DOWN][V]{CTRL_UP] in 'Send Keystrokes'. Bit slower, but . . .
For a full list of the names of the keys, see http://www.tcbmi.com/strokeit/docs/keys.shtml