Xtreme2k,
I'm not sure it's possible to set the in buffer to 1000 and then have flushes every 100, but there are some options that can get you close to that. You can set the Additional Buffer Level checking to 3, and then set the Buffer Level Check Interval to the number of hours:minutes that it would take your cow to do 100 WUs.
The INI parms:
[buffers]
frequent-threshold-checks=3
threshold-check-interval=1:30
The interval is set to hours:minutes, in this example every 1 hour and 30 minutes the client will check for completed work, and if there is, it will flush.
I keep a bit more than 1 day's worth of blocks in my pproxy, and a day's worth at each cow, so if I cannot get blocks from a keyserver, I can go 2 days, and if my pproxy goes down, I've got 24 hours to fix or replace.