Adding a modal popup in a document which is having a flash's object tag may make you in trouble. Because I was having a same kind of problem. To fix it just add another parameter to your object tag (and also to embed tag if any) wmode="opaque". This will allow your popup to show above the flash file.
For those who are using swfobject.js for displaying the flash swf file, just go to shource of the the js file and find this.addParam("quality",q); line. Add another like before or after it,
this.addParam("wmode","opaque"); This will fix your problem.
Hope this will help to you also.