I've never experienced these type of problems, but it requires proper setup. For instance TABLE CONTROL tab > 'Table Control Modes' I have it set to [x] Table Under Mouse + [x] Bring to foreground? This ensures that only the table over which your cursor is placed will be affected by key commands. (note that if you use a HUD and the cursor is placed over any of them the key commands will not work). The program is set up to recognize that you are typing in the chat box or another application, so, in my experience, it's never been a issue. Again this depends on cursor placement. Be sure that if you want to take a note the cursor stays inside the window where you are typing.

You may also want to make sure that none of the '[ ] Automatically click bet button' options are enabled.