I have this problem too, but its usually only at nighttime. My mail will only fetch for one of my email accounts when I ask it to during the day, however at night, while my phone is on my clock radio cradle, it will fetch automatically and I'll wake up to mail on my phone in the morning, making it so I have to double delete all my emails (from phone AND computer).
I dont know if something resets overnight or what and sorry I dont have an answer either, but I wanted to chime in and let you know you're not the only one.