I have looked into this: none of the IPR numbers that you list occur in the InterPro2GO tree that MEGAN currently uses.
This may be because MEGAN's viewer is focused on IPR families. For example, IPR005821 corresponds to a Domain (Ion transport domain), not a family.
An example of something that is contained in MEGAN is IPR022370, which corresponds to the Phosphosulpholactate synthase family.
MEGAN silently swallows IPRs that don't appear in its classification tree, I have added code to warn about this.
I have also added code that allows the user to tell MEGAN how to parse identifiers such as GI numbers or Accession numbers, if desired. This will all be available in 6.7.1 soon.