As I said in my last message, I hadn't touched/changed or added anything to the configuration files.
I figured out a fix myself, so hopefully this will help those who have this problem. It looks like FeelThere made a typo or error in their positioning of the cargo doors in the config file. So if you find this section in the config file for each of the Embraer Regional jets:
[exits]
number_of_exits=2
exit.0 = 0.4, -27.49, -3.68, 4.49, 0
exit.1 = 0.4, -27.11, 3.6, 2.1, 1
and change the third number for 'exit.1' to -3.6 (it's the same value for all three planes), so that it looks like this:
[exits]
number_of_exits=2
exit.0 = 0.4, -27.49, -3.68, 4.49, 0
exit.1 = 0.4, -27.11, -3.6, 2.1, 1