Make sure the game itself is set to windowed mode. If the game itself is set to full screen mode, ISBoxer is going to force it into windowed mode to prevent crashes, but there is currently a bug with the cursor in this mode.

Also, just had this conversation with someone in the ISBoxer Chat Room that reported a cursor issue and the above was not it:
[13:29] <Silence> it's just weird as for instance the Raid button works fine... but on the same window the Who button doesn't
[13:30] <Silence> ok i found it... and i'm not going to say what it was cause it's pretty shaming lol
[13:30] <Silence> as usual
[13:30] <Lax> ok.
[13:30] <Silence> ok fine... the jamba window was exactly behind those tabs/buttons
[13:30] <Silence> somehow it overrules
[13:31] * creo has quit (Ping timeout)
[13:31] <Silence> now i moved it up... and no more problems lol
[13:32] <Silence> so if anyone comes to you with a weird mouse problem... tell em to make sure the jamba team window is nowhere near hehe