Cases Only 1 payment withdrawn from EEA2&EEA1

I wanted to open a post to collect cases that for a joint application (EEA1&EEA2) only 1 payment withdrawn, what happened afterwards? How did you handle?

This is our 2nd time EEA2& EEA1 joint application timeline. (First time is a complete nightmare, posted here: http://www.immigrationboards.com/eea-ro ... l#p1226493 )

1-Aug-2015 submitted
4-Aug-2015 received
5-Aug-2015 only 1 payment withdrawn (both application share exactly same bank account information)
Nothing so far.

I know it is still very early but based on my first "incredible" horrible experience, I can't trust their staff can do basic job. And I might lose my potential job opportunity again if COA letter has been delayed. It is killing me everyday. So I just wanted to know in this case (only 1 payment withdrawn),
1.how many chance we are going to be completely screwed? (they return application... after 1-3 months?),
2.and how many chance 2nd payment will be withdrawn in the future and application back on track?
3. Have you done something useful or helpful if process back on track?

Thought to update my status,

This is extremely strange. I've been told by HO that both payments went through that they have 130 pounds, But in our bank account, there is just only 65 pounds withdrawn.

Does this happened to anybody?