Not showing as being filed

EDIT: 4 times now. 3 owe.  1 gets a refund.  When we check on the irs site for the return with the refund, it says it is being processed.  So, I guess the returns are actually being submitted, but I want my efile confirmation number!

This has happened twice now.  I am curious if anyone else has had it happened or if anyone knows what is going on. 

I submitted a return for efile, and it all seems to be going well.  Then, when I try to check on the status, it acts like I haven't ever submitted it.  It says "marked for EF."  I think I must have accidently canceled it or something, so I try to EF it.  Then, I get the red thumb saying that there is a duplicate number and suggests that I am trying to file a return twice.  This error happens right away, it isn't getting bounced back from the IRS as a duplicate. Both of the returns that this has happened to are to clients who owe money.  Therefore, I can't ask them to check the status through "where's my refund."

Any ideas?  Are the returns filed?  One of them was to have an auto-draft of the amount due, one was going to send in a check. 

Thanks!