Can you post an example showing the issue you describe?
Have uploaded image above and also this is the link: http://bayimg.com/aALLGaACn in case it's too small to see.
On the left screen you can see the flash image where it should be and you can see the hotspot at left. On the right screen you can see that the flash image has been pushed down to the row below.
No matter how much I reduce the flash image or hotspot size, I cannot get both to stay in the correct positions once uploaded.
The actual site is fine at present because I have taken out the hotspot on the live page.
Unfortunately screenshots don't tell us much.
There's no reason for a hotspot to drop the Flash so can you post a link to a page with a hotspot inserted showing the Flash movie dropping.