I doubt that it's the program that's doing this, although not seeing the data file makes it impossible to judge accurately. To me it sounds like BCTool is trying to put everything under one system - which is very inefficient.
Any of the other programs will likely try to do the same thing - bottom line, it's the user's responsibility to separate the data into sites, systems and groups, not the program. For example FreeScan has the option of allocating a RR download to a specific quick key, but it's the user's responsibility to name and organize the sites, systems and groups to the user's liking..
You might want to start by reading the first 4 topics of the following (note that both here and in the wiki, anything in blue is a link)
Uniden DMA FAQ - The RadioReference Wiki
I'm sure BCTool has some sort of editing facility, as well as one to allocate and enable quick keys. That's where I would start, honestly.
best regards...Mike