I seem to remember that if you take them out of the group while doing it it helps. It's probably because when you have it grouped it corrects on the fly which means that any correction in the mastertrack(s) will make changes in all the rest of the group.
Remember not to cut in the track or change the starting point while out of the group because then it cannot be grouped again with the phaselock option on which is imperative when flexing drums.
When you edit transients you only edit the master track (the one with the green Q switched on in arrange) and in all cases I have done it I have basically just editted all the useless transients out. The point is that when you have it grouped with maybe 10-12 other tracks all of these will have to be recalculated everytime you change something which obviously is time consuming and needless. So just edit transients and then put it back into the group and listen.
In your particular case where you want to quantize both the kick and snare you may have to use two tracks for mastertracks since it will be better to use the close mics for quantizing but it's not a big deal if the beat is based around 1-2-3 and 4. The problem is more likely to be in places with drumfills where you have all sorts of timing issues. In many cases fills sound better with a lot of human feel so experiment with maybe leaving them out of the correction (deleting all transients or as many as possible will do the trick).
Are using Flex mode for this type of transient quantizing? It sounds like you're not from what you are describing. Check it out. It will make your life a whole lot easier. Using flex markers or the flex quantizing features (depending on the material) is perfectly suited to the tasks you describe.