You need to create a custom_top under Appl_top. The autoconfig managed setup will always recreate the custom top under appl_top. (/oracle/Appl/apps/apps_st/appl)
custom top you need to create under APPL_TOP and the same location give in topfile.txt [APPL_TOP/admin]
I am hoping that you did created your custom top by following standard oracle recommended steps.
Please perform following to get rid of this issue.
1. Take backup of your application context file.
2. cd $APPL_TOP and you will see 2 different folder with same name. (1 with small xx and another will be in capital XX).
3. Copy everything from/to your actual directory.
4. Stop application tier services.
5. Run autoconfig and then check defaults.env making sure that your actual custom top value is there.
6. Start services if everything looks good.
I hope this helps.
Not: Remember to mark this answer helpful/correct if this resolves your issue.