[development] upgrade d5 to d6 deletes themes and engines from system table

[David Cohen]

After painful investigation, I learned that Drupal was not recognizing
the phptemplate.engine file, because a call to readdir() was simply not
working properly.  It did not return the phptemplate.engine file, until
I touched a new file in that directory, and made a subdirectory.  I did
those two things just to test what was going wrong, and suddenly it did
recognize the file.

But still drupal refuses to find other files.  So for example I don't
see the themes in profiles/custom/themes in my themes list.

I suspect something is wrong at my host.  Has anyone seen anything like
this?