Let's do some troubleshooting to see if there is anything we have both done.
1) How many scripts are loaded total?
2) Do anyone of the scripts have same names? Obviously if they have same names, they come from 2 different directories at least.
3) Do you have anyone loaded from another directory? If you answered 2 yes, then this is yes obviously.
4) How many scripts get unloaded?
5) Does it unload the same scripts each time, or different ones?
6) Are the scripts unloaded always from the bottom of the list?