int64 nMinFeePer = 1000;
I would change this to 1024. It will be much easier to understand if miners announce pricing either as flat value or per KB (i.e. "0.01 BTC per KB").
if (nMinFeeBase / nMinFeePer > 0.00025 * COIN
Since this is for warning on excessively high fees I would increase the threshold. The current threshold ~0.1 US cents even if BTC value increased significantly it would still be sub 1 US cent. I would increase the warning point to 1 bitcent. (> 0.01). While 1 bitcent may be "high" it is likely an intentional value. Someone misunderstanding the concept or units (thinking they are satoshis, fractional BTC or %) would likely put a much higher value and still be warned.
Not sure what is happening here (this bounty gives me more excuse to look into bitcoind sourcecode). My first thought is we are comparing the bitcoind "spam" min fee to the user defined fee? The spam fee depends on coinage though and the processing fee shouldn't. Likely I am misunderstanding so feel free to school me.