Just adding a solution even though this is an old post.
You can brush or apply grease into the groove that the diaphragm sits in to seal things back up. Depending on how much is got messed up you might need to put a weight on part of the diaphragm and apply rtv a section at a time.
Update: 09-18-2013
I don't recommend applying silicone or rtv hi-tack gasket cement (except in extreme situations) as I had a problem with my carburetor again yesterday. The main went out after being parked for 30 min. Took it apart today and found two things:
1. first I removed the diaphragm and dipped in in a clean 1 quart can with "odorless Mineral Spirits" I needed something to dissolve the RTV Hi-Tack but not damage the rubber like carb cleaner. I found that the Hi-Tack is like shelac in that it takes a long time to harden - which is good and bad depending on how and why it is used. After cleaning up I applied dielectric grease (just out of convenience) to the lip or groove where the seal sits. This helped the seal go where it was supposed to and helps form an air tight "vacuum seal".
Start up and the problem was still present - ok on slow jet but no fuel from the main jet. Next, I loosened both boots but left everything else connected and Drained and removed the bowl. Check slow jet and main and everything was fine except... The tip "main jet" was missing. I found it in the bowl. Either I forgot to tighten it or did not tighten it enough. I put everything back together and the scoot is working great. Will give it the real test on the highway.
As a precaution against lean burn I ordered a replacement carb that is by Keihin with electric choke etc, except there IS a re-build kit available unlike the Stock OEM Keihin CVK30 (30mm engine / 50mm air cleaner side).
Also, I found out from a Kymco dealer that sells parts online that the #1 part sold for the OEM Kymco carb is the diaphragm. I suspect that is because people open the door under the seat to adjust the idle and decide to get creative with the carb cleaner on the diaphragm and end up damaging it.
Lessons Learned: pull your carb off and fool with it enough times you start to get pretty good and figuring out what is wrong and making things work.
Also, a malfunctioning carb is often the result of clogging from sitting (in my case from the original owner)... the danger is that when you motor does not get enough fuel it runs lean (hot) and that can damage the motor. Solution: don't hesitate to replace it. I ordered a comparable carb by Keihin for $63 online delivered and will install and post all relevant info: mpg, performance, fit and finish, etc with a link to the supplier and the part #.