Providing some basic info I should have done before:
Inkscape 0.48 (latest official release version, not a bleeding edge dev version)
Windows XP and Vista (occurs on both machines)
The file is a boardgame map that's rather large (at least, for me) - 2588x4345 px
The pattern is actually a ~100x100 bitmap that I've imported and embedded in the file, but placed off to the side of the map edge itself, just for sanity, next to several other imported patterns. This pattern is a thatched hut rooftop that will be used on huts all over the map - with one original hut and many clones. Unfortunately, the original hut is far from the pattern (or rather, the rect containing the pattern) itself, so when I select the Node tool on the original, the pattern transformation handles are waaaay far away. Thus, I wanted to move them closer to the original, which results in the dozens of new patterns being spawned.
I'll post a file when I can - exporting it now, which can take a while at 150 dpi

To answer suv's comment, I don't think it's wrong behavior to create new patterns when they are transformed. Seems like the correct thing to do. I do wonder, though, why Inkscape doesn't wait for me to finish moving the pattern transformation handles before it creates (many) new patterns - like I said in the original post, even a single click-drag-unclick will create dozens of new patterns, which just seems wrong. I expect Inkscape to create ONE new pattern based on what I just did with the mouse. And then,if I've got my Preferences set for storing optimized transformations, I expect Inkscape to roll multiple sequential transformations into one. (There could very well be good reasons for not doing this; I'm just telling you what this user expected from that Preference setting.)
FWIW, the patterns do seem to be mostly translations, and mostly the same size (although unfortunately not obviously related to the size of the pattern or the original filled object themselves). Makes me think that Inkscape is hitting some kind of bounding box upon pattern translation, then dumping the pattern and continuing on. Perhaps not a big deal in most instances, but in my case, the long translation distance is creating dozens-to-hundreds of new patterns that I don't want and don't seem necessary.
I'm not a coder, but the fix seems to be either removing whatever condition causes Inkscape to dump patterns in progress of transformation, or giving Inkscape the option to optimize the final transformation based on everything that happened between mouse-down and mouse-up.
Thanks for the help. If nothing else, it's good to know I'm not crazy
