This is hard (for me :-) ) to visualize as there are so many variables that could be affecting this.
A random suggestion. I think if you started again and JUST used the "overall finacial coefficient" to get to the salary structure you want, that should adjust everything related to the financials. That's just the one setting to worry about, instead of a lot of manual work in the back end.
Possibly you've missed adjusting something that is causing problems even though you feel good about the default salaries.
Here's the page of the online manual with more...
http://manuals.ootpdevelopments.com/...ncial_settings
Just another 2c opinion for you!