They won’t split when the funds are received, but when they are minted or sent. i.e.: you can force a split by sending shares.
Having two clients both minting on the same set of addresses (technically, transaction outputs) is setting up for a problem, due to this functionality: https://www.peercointalk.org/index.php?topic=1956.55;wap2 … the TL;DR-- at best you will get a lot of stale blocks, tying up outputs unnecessarily.
I’ll assume the 50k NSR are received as one transaction output (i.e.: they are not split)
In this example, the wallet with 10k chunks will try to mint the one output. When it’s successful, it will create a transaction with 5 outputs of 10k NSR in size.
If at the same time the splitshareoutputs=50k wallet is minting (ignoring for a moment the problem from above), and it also scores, it will create one output of 50k.
If both blocks are found and sent on the network at the same time (very likely, based on how the stake algorithm works), at best only one will win.
So both clients would have thought they ‘minted’ the singluar non-split 50k input transaction (that you received), and the 50k NSR are tied up for the coinstake period.