Did you figure out what the correct postage was? I found that not even the local postmaster(not just the clerk but the boss) does not know how to correctly figure postage. When I disputed a fee she actually had to look in the master book because "she had no idea what the correct postage was"!

I know that if the envelope is larger than allowed for a letter they almost always charge the package rate instead of the large envelope rate. It is just easier for them.