This is likely happening because of the "improved" IIF importing process Intuit added to QB 2019 and newer versions. It included a plethora of bugs, few of which Intuit has fixed over the last three version years. And it is very, very slow at the same time.
To get QuickBooks to honor what is in the IIF file instead of recording whatever it feels like, follow these recommendations:
BRC QuickBooks 2019+ IIF Import Changes and Recommendations
