adding a section is a very simple task with lordpe.
when you add a new section in a exe you should control the following things:
1) section do not overlap
2) the virtual size of each section must fill entirely the range between one
section and the other.
Lordpe is a very useful tool as it can do it automatically.
In particular it can be forced to do the step 2) with the option recontruct pe.
you can post the new section header table so i can show you where the problem is (grab the section header with lordpe or some other tool).