In regards to different scanner programs--well, depending on manufacturer, you're going to have different options.
Butel and ScanStar have been options for the Uniden crowd (along with a number of other options); until fairly recently, pretty much *the* option for GRE kit was Starrsoft's WinXX programs (the Pro-92, whose transfer format was reverse-engineered, had considerably more options including open source offerings; the situation with the PSR-500 is starting to look very similar, especially as GRE is willing to work with developers in providing specs (and they should be commended for this!), and no less than three commercial development packages have already been announced and are in various stages of development).
I have always gotten the impression with ScanStar that they essentially "shoehorned" the GRE Radio Shack kit in as an afterthought--the program is designed for Uniden scanners primarily, and as an afterthought tries to be a general "swiss army knife" programming tool for a number of other manufacturers. There are, alas, compromises to be had in this.
It *would* have actually been interesting to see if Signal Intelligence would have done anything with the new GRE kit coming out (as (among other things) there are nifty features like live trunking info dump/monitoring through the PC/IF interface, the ability to use the PC as a remote control headend, etc. that are more similar to Uniden offerings); still, though, I have a feeling that the needs of GRE scanner owners are better met with programs designed to work with what the GRE scanners do well (and so far, Don Starr has been best of breed on that, though Mike Vander Veer's offerings in this regard are giving Don some real competition

).
A good parallel on this is with PCs and Macs (and their respective operating systems). Yes, you *can* in theory use an Intel-based Mac to run Windows (for the stuff that MacOS X doesn't have ported to it yet). You can even (with tools like Parallels, etc.) run Windows apps under MacOS X itself. It still feels kludgy as all get out, though, and generally if given a choice MacOS X users will choose a Mac-native tool to do what they need to do (especially if the tool relies on Windows-specific stuff that won't work under MacOS X) because it *works better for Macs*.
You can run MacOS X on PCs with a whole lot of hackery, too. You can't run MacOS X apps, admittedly, unless you DO put MacOS X on--but it's still clunky. MacOS X was never really designed for PCs in the first place.
(And then there's Linux, but that's another ball of wax not relevant to the analogy

I don't know of any scanner programs that attempt to fit a "Linux" role of being able to do a few things well across scanner manufacturers. Maybe Butel

)
Anyways, software programs for different scanner manufacturers are much like that. Unless they are designed "Linux style"--that is, from the get-go to do a few things well across multiple scanner families--it's always going to feel kludgy using scanner tools that cover GRE kit but which were designed with Uniden users in mind
(And yes, this is coming from someone who uses GRE kit, which in its own way is kind of the "MacOS of the scanner world"

And who is hoping someday to get some native tools out for MacOS X and Linux for working with our little "different" scanners

)