Reliable custom Windows shortcut keys?

I have global Windows shortcut keys assigned to several different cmd.exe instances. I do this by creating shortcuts to cmd.exe on my desktop, and assigning each one a unique shortcut key (for example, CTRL + SHIFT + U). Pretty basic stuff. I'm using Win2K8 (R1 and R2).

This works just fine... most of the time. But with infuriating regularity, sometimes it doesn't. Or it will work with a long delay (many seconds). It doesn't matter what app currently has focus (it can even be one of the command prompts). It doesn't matter what keys I assign (I've tried a few variations of WIN, CTRL and SHIFT). I did notice that this is often, but not always, correlated with explorer.exe struggling in some way or another (say, an explorer window opened to a file share that's unavailable, or an app being unresponsive, or whatever). In other words the shortcut key handling appears to be very sensitive to unrelated system activity. Note that whenever I have this problem I can always successfully ALT + TAB to the window I want to get to, but that's tedious.

I use the shortcuts to these command windows hundreds of times a day so even a 1% failure rate becomes really annoying.

Is there a way to fix this, or is there some third-party utility out there that will RELIABLY intercept custom key combinations to bring focus to whatever apps I want, in a way that is independent of other system activity?

ADDENDUM:

There is a property of the Windows shortcuts that I would not want to lose if switching to a third-party hotkey tool: Windows shortcuts are idempotent. Once you've launched a shortcut to some app, pressing the shortcut key combo again takes you to the already launched process - it does not launch a new process.