i've noticed this for sometime and it bothers me a bit since i use SC not just as a screenshot tool but also for managing the captured images.
it's like this, if i capture 'selected region' of an area in Firefox, SC will name it as "Firefox.exe-01_08_2010_001.png" which is good since that is how i've defined it in the 'File Naming Template'. however if the next capture of the same Firefox window is invoked via 'Grab Repeat Last Size+Pos', then the file will be named "Screenshot Captor-01_08_2010_001.png" (see pic) which is technically correct but it disrupts my work-flow.
what i suggest is that if a screen-capture is within a range of x seconds or minutes of the previous capture, then filename should continued as a sequence, disregarding 'File Naming Template'. in this case, the 2nd capture will be "Firefox.exe-01_08_2010_002.png".