On-Boost Flutter is different from flutter that happens when you let off the throttle and the throttle plate closes. On-Boost Flutter is surge, where the turbo is operating in an unstable area of the turbocharger's compressor map. A compressor bypass valve such as a Diverter Valve or BOV have nothing to do with how this characteristic happens when the valve is closed. Either way, the turbo is producing more airflow than the engine can ingest, resulting in backflow through the compressor section of the turbo. OEM diverter valves have built-in leaks in their valving mechanism as a workaround to surge, the only problem is that the leak exists in all operating conditions, low boost, high boost, etc. At the end of the day, you will need to unload the compressor in order to eliminate On-Boost Flutter (surge).
Solutions: Run a very light spring in the Synchronic device. This will allow you to leak the boost slightly as boost onset happens and will close the valve completely under WOT or full boost conditions. This is a necessary solution for some cars (Evo) where part throttle on-boost flutter results in vehicle instability due to varying signals that the MAF is receiving.
How to Test: You can test if the Synchronic compressor bypass valve (CBV) is the culprit by eliminating it from the equation. Use a thick piece of rubber, to block off the discharge or inlet port of the CBV so that the system acts as though there isn't a device at all. If you still have on-boost flutter, then it is a characteristic of your turbo and how it matches up with your engine setup (cams, injectors, fuel, etc.). Alternatively, you can remove the pre-load adjuster from your CBV and install a bolt down far enough to hold the actuating piston in place and not moving. This will also have a similar effect.
Why do I have on-boost flutter now, I didn't have it before?: Environmental conditions have a great effect on whether or not a turbo will surge. Higher altitudes (elevation) will trigger surge. You will also have a higher incidence of surge when the air density is increased. Anecdotally, you will also find that turbos that have more wear on them will also tend to flutter more. The type of wear will vary and can be anything from an increase in compressor blade tip to housing clearance, all the way to slight bearing wear.