I apologize for the reply to an apparently old question. I worked for a few months with various engineers and ended up with Michal and a second set of developers.
We found that after all permissions on files are correct the "insufficient read access privileges to /etc/named.conf" is still encountered.
In the end the problem is that IPAM cannot handle special characters in the bash prompt (~ [ ] etc.)
This is why running the commands by hand gives expected reults.
When using an account configured just for IPAM, I just changed the bash prompt and it started working the prompt I used:
export PS1="\u$ "
Apparently, the $ is an acceptable special character.