I get this same problem when using the Alt key as part of a hotkey combination with my macros, though to be honest I haven't tried out their keyboard accelerators yet. In general, leave the Alt key out of keyboard shortcuts for this very reason. It's conventional function these days is simply to open the main menu toolbar and its mnemonics.
Having said this, your problem may simply be that the accelerator won't function effectively until the Alt key is released, which leaves the shortcut hanging until you realize this. Even then, making the Alt key a hotkey for a shortcut that already contains an Alt key combination can be asking for trouble. I don't know about PB's accelerators, but at least AutoHotkey allows me to program my way out of this mess (which I won't go into here, but read the Keys section in its manual), also using other keys such as the left or right Windows key and the Applications key which normally opens the context menu. It depends on what your keyboard contains, which is determined by your hardware and OS.
PB 188.8.131.52 on Windows XP, J-1.6.0_17