There is an "Alert" on this subject. Here's the link, Solved: 1040-ES payments not being withdrawn - Intuit Accountants Community 

For my clients I had to call the IRS and cancel the Q2 payment, and then go online to the IRS Direct Payment website and schedule the Q1 payment to be paid immediately, and then schedule the Q2 payment for June 15th.

This works, BUT ONLY for about 10 clients and then the web page tells you you've reached your limit and bumps you off. GRRRRR. I even tried another browser, that didn't work, so I went to another computer (same office) and that didn't work either, now I have to sit here for an unknown amount of time before I can go and finish the job. GRRRRRR.

Another issue. The "Look up tool" doesn't complete the job... I used it and come up with a dozen clients, the list DID NOT include my own return nor my parents' which both have the same issue. I called the IRS e-file Payment Services 24/7 at 1-888-353-4537, and cancelled my clients Q2 payments and then asked him to verify mine and my parents and sure enough, the same issue. So beware, the look up tool may not show all affected clients. GRRRR!!!!!

It really is sad that we have to go through all of this! Intuit and the IRS should come up with a solution that resolves the issue without us having to do all of this, I have been working on this for for about 4 hours and gotten through 10 clients. Not to mention what we are going to have to do next year because you know the IRS is going to charge late fees for not having estimateds paid on time.