Hiya Band,

I must admit when I'm doing conforming clothing I tend to cheat, I don't use the PHI process because it's too easy to miss something and run into problems like the one you describe.  Generally when I'm doing conforming clothing here's how I do it:

Step 1:  Load the default figure the clothing is for in Poser in it's default pose.  It's usually best to use the default model that is "bare", meaning the one that doesn't have any morphs or anything with it.  It's not essential mind you, but it will speed up the process somewhat as it takes longer to load them.  Just be sure not to move or change the position of the default figure the clothing is for in anyway, leave it in exactly the position it was in when it was loaded.  The reason for this, you'll be using this as a reference to line up your clothing, and when you go to add bones to your cloths you'll be doing so by loading this exact same figure in the setup room, which has the effect of pulling in the bones from that figure in the exact same place they are in your current reference model.

Step 2.  Import the prop for the clothing item (in this case your boots) and then position them so they fit properly on the model in it's default Pose.

Step 3:  With the prop for the clothing selected, enter the setup room - then in the figures tab in your library click on the same base model (ie V3, V4, M3, etc) you used to load the default figure the clothing is for, this will recreate the exact bone structure of the default figure inside your current object file.

Step 4: Return to the Pose room, and save a copy of your newly created figure.  You'll probably need to change some names under properties so your figure won't show up as "Figure 1" and should it be necessary you'll might have to redo the auto grouping on the mesh slightly  for more realistic bends, but usually it does a pretty good job of this on it's own overall.

Hope that helps.