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hmm, that sound veeeeeeeeeeeeery strange, i am not aware about your previous installations, have you installed to a clean folder ? i mean just unpacked and clicked the.exe

so, what do you mean by "access the help file"?

 
  - what is the link of the download

beside of this, apophysis is a quite abandoded and rather dead project, no real developer is maintaining it, please use more active flame fractal editors,
for example:

- chaotica - it can easily load and edit flame fractals made with apophyis, it is under active development, and has a very decent user interface
http://www.chaoticafractals.com/

- jwildfire - as well a very decent and advanced flame fractal editor, grab it here:;
http://www.andreas-maschke.com/?page_id=42

both programs are actively developed and far more capable than apophysis - believe me - and i think both programs can load apophysis files, so, give them both a try, they are both very good flame fractal editors, actually, apophysis is more like a proof of concept, rather than a worked out piece of software, and apophysis has not been updated by the original developer for - i think - more than ten years, so, either get it working or describe more detailed what kind of plugins your are talking about...