I have had the same kind of problems, here is what i do to make the export of my files:
1. Open the part you want to make a igs / stp of.
2. Right click on the body and click copy (keep the window open)
3. Make a new part.
4. Right Click on the new part and select paste special
5. In the paste special dialog box select AsResultWhitLink and click OK
6. Now you got a new solid whit link to the previous part, right Click on the solid and select Isolate to break all links.
7. Save the new part whit a different name.
8. Close Catia.
9. Open Catia Again
10. Open the new part (the one whit the solid whiteout link)
11. Save this part as igs or stp
This is the way i have been lucky to make the most of my iges or step files.
Hope that it helps.
Best regards