We may have a workaround in trunk. I have applied a patch proposed by Kiran, and after having injected 11 000 DN in a memberOf attribute, the MasterTable has reasonably grown to 3 Mb.
However, it takes a hell of a time to inject data this way, and it takes more and more time when we add more and more entries. For instance, adding the first 100 DN cost only 400ms, but adding 100 DN when we already have 11 500 DNs costs more than 20 seconds.
I have also applied a patch to partially fix this problem (without this patch, we would not talk about 20 seconds, but more probably 20 minutes !), but there are many inefficient operations done when modifying an entry (10 lookups are done, representing 2/3 of the time needed to proceed).
We will first apply the two patches, and keep going on investigation.