> > "C:\Program Files\ZTreeWin\ZTW.EXE" *%%str1%%*%%str2%%*.*
> > *%%str2%%*%%str1%%*.*
> >
> > the first instance till I quit the second one? I tried adding "start
> "
> > at the start of the second line, but then it doesn't like the filter
> parameters.
>
> The 'start' command takes the first quoted argument to be the title
> of the target window. Try start ""
> "C:\Program Files\ZTreeWin\ZTW.EXE" ...etc instead.

That works nicely, thanks. So the script is now:
rem #ztset str1 String 1:
rem #ztset str2 String 2:
Start "" "C:\Program Files\ZTreeWin\ZTW.EXE" *%%str1%%*%%str2%%*.* *%%str2%%*%%str1%%*.*

If you really needed to have the filter set in the first ztree instance, you could go into the history of the second instance, press F3 to save the history. Then press F4 in the history of the first instance to load it up. Fiddly.

Is there any way to get the second instance to start with a ztree icon in the taskbar? For me it's showing as a cmd .exe icon.