Can you provide some more info?
What kind of Emitter (legacy particles or PFlow), what is the end result and how is it different from the expected result? Screenshots, animation or a scene file are welcome.
Krakatoa is supposed to save the particles in world space exactly as calculated by Max. Of course, moving an emitter along a path does not automatically move the particles along the path (in the case of the legacy particles like SuperSpray, there is a space warp for that, for PFlow it is doable via scripting).
Once you have saved the PRT sequence, do the particles loaded by the PRT Loader when set to 100% in the viewport match the positions of the particles of the source system? (normally they should - show us a screenshot if they don’t align). You can also deform particles loaded by a PRT Loader using a Path Deform to create a particle cloud following a path after the saving which might be easier and would be a lot more flexible.

