Since merged mining began on site I've found my system has become unstable when mining btc. Is seems fine on my backup site for mining.
Of course there was big problems with connectivity due to DDoS attacks. Not sure if you counted it. There was also few issues with backends two weeks back when pool started with merged mining, but then I disconnected problematic pools and thanks to recent update of backends, merged mining does not affect mining at all; now it's definitely not an issue. Thanks to my pool monitoring I can tell that now is pool in excellent condition.
Recently you said the whole network is used though for merged mining could this be causing issues for those of us that aren't interested in namecoins? If it is why not offer an opt out from merged mining for those of us that don't wish to mine namecoins?
Merged mining, when done properly, cannot affect "non-namecoin" users. And I'm absolutely sure that merged mining is working great. Technically merged mining is only small patch for bitcoin backend, nothing what you can 'opt out'. If you're not interested in namecoin, it won't affect you at all and you even don't need to know that your hashrate is 'used for merged mining'. However if you claim your namecoin address, you'll get bunch of coins on top of your bitcoin income.