I don't think I saw this infor mentioned earlier and I am new to the site so I don't know what you are running exactly. I know it's a blow through style twin turbo but don't have the details.
What size turbo's are you running?
Single or dual BOV(s)?
What size BOV(s) are they?
Where is it (are they) located?
Diverter style or open atmosphere style?
I'm thinking your BOV(s) is (are) either to small, or not set up properly.
With my car, I am going to be running a large single (T91 on a 348ci LS1). I am planning on running a dual BOV set up. One just before teh Throttle body and te other further upstream towards the turbo. I have been told to do it this way by a few different well known turbo companies.
There comes a point when you are moving just too much air for a single BOV to reduce intake pressure enough.
BOV's don't typically stay open for long once you let out. They make a quick release of the pressurized intake system. If your BOV is not keeping up with the turbo, you could have issues as described on a blow through set up. A injected setup wont experience this problem of often.