I honestly think you're reading too much into this.
This isn't rocket science; it's voice acting. He's entitled to slip up, he's entitled to make a mistake, and, more importantly, he's entitled to sound 'flat'.
Whilst it's possible that the 'personality change' (always seemed like a change in motives and means, really) could have influenced the change in overall tone, it's far more likely that this is human error. Could be a combination of both. Personally, no offense to Quinton Flynn, I'm gunning for simple mistake, the latter. Latter; he may have purposely changed his tone, and fell short of whatever he was going for.