This seems to have started with the latest beta, though I'm not absolutely positive of that.
The machine is a 1st generation Mac Pro 2GHz, 9GB of RAM, OS 10.6.2, PM v. 4.6.3 beta 1, Lightroom 2.6 (and LR3 beta).
I import and keyword my photos with PM, then import into Lightroom. I experienced issues last year when Lightroom wasn't stripping leading/trailing spaces from keyword hierarchies (hadn't realized there were spaces on either side of PM's standard "pipe" separator character), but eventually got that sorted. Had a small panic attack when a recent version of PM started putting the spaces back in, but was assured that it was only for display and that the spaces weren't actually exported in the hierarchy - everything was working fine.
After updating to 4.6.3 beta 1, I started getting duplicate hierarchies again, with the new entries showing leading and trailing spaces in Lightroom. Strangely, the keywords are now being written to both the proper spots in the hierarchy (with no spaces) and the new hierarchies (with spaces), so I can just delete the duplicated hierarchies with no further problems, but it's still a pain.
I just tried to duplicate the issue by switching between 4.6.2.1 and 4.6.3, and everything worked fine (of course!), but it definitely didn't yesterday. Off to scratch my head........