I can't believe I'm thinking this...

[J. Stew]

You could make a conscious effort to get back into your normal 'good poker-playing mentality' when you go from bonus clearing to normal play. I think if you're aware you're game is slipping that is good and you can correct it by being attentive to it. If bonus clearing is actually hurting your winrate, counting what you're clearing, that's obviously bad, but if you are having trouble transitioning between mentalities then you can sort that out I think.